diff -Nru beast2-mcmc-2.6.6+dfsg/build.xml beast2-mcmc-2.6.7+dfsg/build.xml
--- beast2-mcmc-2.6.6+dfsg/build.xml	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/build.xml	2022-04-04 07:18:36.000000000 +0000
@@ -269,10 +269,10 @@
 
 
     <!-- Release -->
-    <property name="version" value="2.6.6" />
-    <property name="version_number" value="2.6.6" />
+    <property name="version" value="2.6.7" />
+    <property name="version_number" value="2.6.7" />
     <property name="release_dir" value="release" />
-    <property name="copyright" value="Beast 2 development team 2011-2021" />
+    <property name="copyright" value="Beast 2 development team 2011-2022" />
 
     <property name="BEAST_name" value="BEAST" />
     <property name="beast_name" value="beast" />
@@ -847,7 +847,7 @@
         <copy file="${common_dir}/README.txt" todir="${Mac_package_dir}" />
         <copy file="${common_dir}/LICENSE.txt" todir="${Mac_package_dir}" />
 
-        <echo message="Creating BEAST.app ..." />
+        <echo message="Creating BEAST.app using ${stubfile} ..." />
 
         <!-- create a jar bundle for the mac -->
         <jarbundler dir="${Mac_package_dir}"
@@ -1134,7 +1134,7 @@
     </target>
 
     <!-- no jre -->
-    <target name="mac">
+    <target name="mac" unless="file.exists">
         <delete dir="${Mac_package_dir}" />
         <!--<delete file="${Mac_dir}/pack.temp.dmg"/>-->
         <delete file="${Mac_dir}/${beast.dmg}"/>
@@ -1160,9 +1160,11 @@
             <fileset dir="${common_dir}/doc" />
         </copy>
 		-->
-
+<!--        <property name="stub" value="release/Mac/stub/3-0-3/universalJavaApplicationStub" />-->
+        <property name="stub" value="release/Mac/stub/3-2-0/universalJavaApplicationStub" />
+        <available property="file.exists" file="${stub}"/>
         <antcall target="bundle">
-            <param name="stubfile" value="${Mac_dir}/universalJavaApplicationStub"/>
+            <param name="stubfile" value="${stub}"/>
         </antcall>
 
         <antcall target="codesign"/>
@@ -1170,17 +1172,21 @@
         <antcall target="dmg"/>
 
         <property environment="env"/>
-        <property name="dmg.path" value="../../tmp/${BEAST_name}.v${version}.dmg" />
+        <property name="dmg.fn" value="${BEAST_name}.v${version}.dmg" />
+        <!-- name is fixed to BEAST v2.?.? in createdmg.sh -->
+        <!-- rename to BEAST.v2.?.? -->
+        <move file="${Mac_dir}/${beast.dmg}" tofile="${Mac_dir}/${dmg.fn}"/>
 
-        <copy file="${Mac_dir}/${beast.dmg}" tofile="${dmg.path}" />
+        <property name="dmg.path" value="${user.dir}/tmp" />
+        <copy file="${Mac_dir}/${dmg.fn}" todir="${dmg.path}" />
 
-        <echo message="Mac version release is finished." />
+        <echo message="Mac release is finished. ${dmg.path} is created." />
 
-        <echo message="Go to ~/tmp to make notarization" />
+        <echo message="Go to ${user.dir}/tmp to make notarization" />
 
-        <antcall target="notarization">
-             <param name="dmg.path" value="${dmg.path}"/>
-        </antcall>
+<!--        <antcall target="notarization">-->
+<!--             <param name="dmg.path" value="${dmg.path}"/>-->
+<!--        </antcall>-->
 
     </target>
 
@@ -1204,9 +1210,11 @@
                 <exclude name="benchmark/**" />
             </fileset>
         </copy>
+        <!-- /usr/libexec/java_home -V-->
+        <!--  brew upgrade adoptopenjdk/openjdk/adoptopenjdk8 -->
         <property name="openjre" value="/Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home/jre"/>
         <exec executable="cp">
-		    <arg line="-R ${openjre} ${Mac_package_dir}/jre1.8.0_262"/>
+		    <arg line="-R ${openjre} ${Mac_package_dir}/jre1.8.0_292"/>
 		</exec>
         <!-- Deprecated JavaAppLauncher -->
 <!--        <exec executable="gcc">-->
@@ -1217,9 +1225,11 @@
             <fileset dir="${common_dir}/doc" />
         </copy>
 		-->
-
+        <!--        <property name="stub" value="release/Mac/stub/3-0-3/universalJavaApplicationJREStub" />-->
+        <property name="stub" value="release/Mac/stub/3-2-0/universalJavaApplicationJREStub" />
+        <available property="file.exists" file="${stub}"/>
         <antcall target="bundle">
-             <param name="stubfile" value="${Mac_dir}/universalJavaApplicationJREStub"/>
+            <param name="stubfile" value="${stub}"/>
         </antcall>
 
 <!--        <delete file="${Mac_package_dir}/BEAST.app/Contents/MacOS/JavaAppLauncher"/>-->
@@ -1246,17 +1256,20 @@
         <antcall target="dmg"/>
 
         <property environment="env"/>
-        <property name="dmg.path" value="../../tmp/${BEAST_name}_with_JRE.v${version}.dmg" />
-
-        <copy file="${Mac_dir}/${beast.dmg}" tofile="${dmg.path}" />
-
-        <echo message="Mac with JRE version release is finished." />
-
-        <echo message="Go to ~/tmp to make notarization" />
-
-        <antcall target="notarization">
-            <param name="dmg.path" value="${dmg.path}"/>
-        </antcall>
+        <property name="dmg.fn" value="${BEAST_name}_with_JRE.v${version}.dmg" />
+        <!-- name is fixed to BEAST v2.?.? in createdmg.sh -->
+        <!-- rename to BEAST_with_JRE.v2.?.? -->
+        <move file="${Mac_dir}/${beast.dmg}" tofile="${Mac_dir}/${dmg.fn}"/>
+        <echo message="Mac release is finished. ${dmg.path} is created." />
+
+        <property name="dmg.path" value="${user.dir}/tmp" />
+        <copy file="${Mac_dir}/${dmg.fn}" todir="${dmg.path}" />
+
+        <echo message="Go to ${user.dir}/tmp to make notarization" />
+
+<!--        <antcall target="notarization">-->
+<!--            <param name="dmg.path" value="${dmg.path}"/>-->
+<!--        </antcall>-->
 
     </target>
 
diff -Nru beast2-mcmc-2.6.6+dfsg/debian/changelog beast2-mcmc-2.6.7+dfsg/debian/changelog
--- beast2-mcmc-2.6.6+dfsg/debian/changelog	2021-08-23 14:40:39.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/debian/changelog	2022-04-22 13:59:01.000000000 +0000
@@ -1,3 +1,10 @@
+beast2-mcmc (2.6.7+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 2.6.7+dfsg
+  * Reworking debian/copyright
+
+ -- Pierre Gruet <pgt@debian.org>  Fri, 22 Apr 2022 15:59:01 +0200
+
 beast2-mcmc (2.6.6+dfsg-2) unstable; urgency=medium
 
   * Lowering heap size on 32 bit architectures
diff -Nru beast2-mcmc-2.6.6+dfsg/debian/copyright beast2-mcmc-2.6.7+dfsg/debian/copyright
--- beast2-mcmc-2.6.6+dfsg/debian/copyright	2020-09-30 06:08:29.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/debian/copyright	2022-04-22 13:53:50.000000000 +0000
@@ -6,10 +6,116 @@
 Files-Excluded: */*.jar
 
 Files: *
-Copyright: 2002-2011 Alexei Drummond and Andrew Rambaut
-License: LGPL-3+
+Copyright: 2002-2011 Alexei Drummond, Andrew Rambaut, and Walter Xie
+License: LGPL-2.1+
+
+Files: release/Mac/stub/*
+Copyright: 2014-2021 Tobias Fischer
+License: Expat
+
+Files: src/beast/app/tools/LogCombinerDialog.java
+       src/beast/app/treeannotator/TreeAnnotator.java
+       src/beast/app/treeannotator/TreeAnnotatorDialog.java
+       src/beast/evolution/alignment/distance/*
+       src/beast/evolution/branchratemodel/*
+       src/beast/evolution/likelihood/BeagleTreeLikelihood.java
+       src/beast/evolution/speciation/*
+       src/beast/evolution/tree/*
+       src/beast/math/*
+       src/beast/util/FrequencySet.java
+       src/test/beast/beast2vs1/*
+Copyright: 2002-2010 Alexei Drummond and Andrew Rambaut
+License: LGPL-2+
+
+Files: src/beast/evolution/operators/JointOperator.java
+       src/beast/evolution/tree/TreeTraceAnalysis.java
+       src/beast/app/draw/IntegerListInputEditor.java
+       src/test/beast/evolution/tree/RandomTreeTest.java
+Copyright: 2012-2015 Tim Vaughan
+License: GPL-3+
+
+Files: src/beast/core/parameter/GeneralParameterList.java
+       src/beast/app/beauti/JPackageRepositoryDialog.java
+Copyright: 2013-2014 Tim Vaughan
+License: LGPL-2.1+
+
+Files: src/beast/evolution/alignment/Sequence.java
+       src/beast/evolution/alignment/Alignment.java
+       src/beast/evolution/likelihood/TreeLikelihood.java
+       src/beast/evolution/likelihood/ThreadedTreeLikelihood.java
+       src/beast/evolution/likelihood/ThreadedLikelihoodCore.java
+       src/beast/evolution/likelihood/LikelihoodCore.java
+       src/beast/evolution/operators/Exchange.java
+       src/beast/evolution/operators/TreeOperator.java
+       src/beast/evolution/operators/SubtreeSlide.java
+       src/beast/evolution/operators/Uniform.java
+       src/beast/evolution/operators/WilsonBalding.java
+       src/beast/evolution/operators/ScaleOperator.java
+       src/beast/evolution/tree/Node.java
+       src/beast/evolution/sitemodel/SiteModel.java
+       src/beast/evolution/substitutionmodel/Frequencies.java
+       src/beast/evolution/substitutionmodel/TN93.java
+       src/beast/evolution/substitutionmodel/GeneralSubstitutionModel.java
+       src/beast/evolution/substitutionmodel/SubstitutionModel.java
+       src/beast/evolution/substitutionmodel/HKY.java
+       src/beast/util/MersenneTwisterFast.java
+       src/beast/util/PackageManager.java
+       src/beast/util/XMLParserException.java
+       src/beast/util/JSONParserException.java
+       src/beast/util/XMLProducer.java
+       src/beast/util/ClusterTree.java
+       src/beast/util/TreeParser.java
+       src/beast/util/JSONParser.java
+       src/beast/util/XMLParser.java
+       src/beast/util/PackageDependency.java
+       src/beast/util/Randomizer.java
+       src/beast/core/Distribution.java
+       src/beast/core/Input.java
+       src/beast/core/Description.java
+       src/beast/core/BEASTObject.java
+       src/beast/core/State.java
+       src/beast/core/util/CompoundDistribution.java
+       src/beast/core/MCMC.java
+       src/beast/core/Citation.java
+       src/beast/core/BEASTInterface.java
+       src/beast/core/Logger.java
+       src/beast/app/BeastMCMC.java
+       src/beast/app/DocMaker.java
+       src/beast/app/ModelBuilder.java
+       src/beast/app/draw/Document.java
+       src/beast/app/draw/InputShape.java
+       src/beast/app/draw/Selection.java
+       src/beast/app/draw/HelpBrowser.java
+       src/beast/app/draw/Arrow.java
+       src/beast/app/draw/Shape.java
+       src/beast/app/draw/ModelBuilder.java
+       src/beast/app/draw/BEASTObjectShape.java
+       src/beast/app/draw/TrackPoint.java
+Copyright: 2010 Remco Bouckaert <remco@cs.auckland.ac.nz>
+License: LGPL-2+
 
-Files: src/org/apache/commons/math/*
+Files: src/beast/app/treeannotator/TreeSetParser.java
+Copyright: 2011 Remco Bouckaert <remco@cs.auckland.ac.nz>
+License: GPL-2+
+
+Files: src/beast/app/treeannotator/RealNumberField.java
+Copyright: 2009 JAM Development Team
+License: LGPL-2.1+
+
+Files: src/beast/core/Operator.java
+Copyright: 2011 BEAST2 Core Team
+License: LGPL-2+
+
+Files: src/beast/core/parameter/BooleanParameter.java
+       src/beast/evolution/operators/BitFlipOperator.java
+Copyright: 2010 Joseph Heled jheled@gmail.com
+License: LGPL-2+
+
+Files: src/beast/math/MachineAccuracy.java
+Copyright: 2010 BEAST II Developer Group
+License: LGPL-2+
+
+Files: src/org/apache/*
 Copyright: 2003-2016 The Apache Software Foundation
 License: Apache-2.0
 
@@ -17,8 +123,11 @@
 Copyright: 2010-2015 The Android Open Source Project
 License: Apache-2.0
 
-Files: src/beast/app/treeannotator/TreeSetParser.java
-Copyright: 2011 Remco Bouckaert <remco@cs.auckland.ac.nz>
+Files: debian/*
+Copyright: 2011-2012 Andreas Tille <tille@debian.org>
+           2022-2022 Pierre Gruet <pgt@debian.org>
+License: LGPL-3+
+
 License: GPL-2+
  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
@@ -33,10 +142,6 @@
  On Debian systems, the complete text of the GNU General Public
  License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
 
-Files: src/beast/app/draw/IntegerListInputEditor.java
-       src/beast/evolution/operators/JointOperator.java
-       src/beast/evolution/tree/TreeTraceAnalysis.java
-Copyright: 2012-2015 Tim Vaughan
 License: GPL-3+
  This program is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
@@ -51,10 +156,6 @@
  On Debian systems, the complete text of the GNU General Public
  License version 2 can be found in `/usr/share/common-licenses/GPL-3'.
 
-Files: debian/*
-Copyright: 2011-2012 Andreas Tille <tille@debian.org>
-License: LGPL-3+
-
 License: LGPL-3+
  This program is free software: you can redistribute it and/or modify
  it under the terms of the GNU Lesser General Public License as published by
@@ -91,3 +192,30 @@
  .
  On Debian systems you can find the full text of the Apache 2.0 license
  at /usr/share/common-licenses/Apache-2.0.
+
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to
+ deal in the Software without restriction, including without limitation the
+ rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+ sell copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
+ IN THE SOFTWARE.
+
+License: LGPL-2+
+ On Debian systems the full text of the LGPL-2 can be found in
+ /usr/share/common-licenses/LGPL-2
+
+License: LGPL-2.1+
+ On Debian systems, the complete text of the GNU Lesser General Public
+ License version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’.
diff -Nru beast2-mcmc-2.6.6+dfsg/Dockerfile beast2-mcmc-2.6.7+dfsg/Dockerfile
--- beast2-mcmc-2.6.6+dfsg/Dockerfile	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/Dockerfile	2022-04-04 07:18:36.000000000 +0000
@@ -6,16 +6,21 @@
 # To run the tests, use
 #   docker run beast_testing
 #
+# To run just the core tests, use
+#   docker run beast_testing test-core
+#
 # To run the tests interactively, use
-#   docker run -it -p 5900:5900 beast_testing /bin/bash
+#   docker run --entrypoint /bin/bash -it -p 5900:5900 beast_testing
 # This will give you a shell in the container. From this
 # shell, run
-#   vncserver $DISPLAY -geometry 1920x1080; ant -f build-testing.xml
+#   ./entrypoint.sh
+# or
+#   ./entrypoint.sh test-core
 #
 # The previous command exposes the VNC session, so while the
-# BEAUti test suite is running you can run a VNC viewer and
-# connect it to localhost (password: password) to observe
-# the graphical output of these tests.
+# BEAUti test suite is running you should be able to run a
+# VNC viewer and connect it to localhost (password: password)
+# to observe the graphical output of these tests.
 
 FROM openjdk:8
 
diff -Nru beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/beast1/testEBSP-b1.xml beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/beast1/testEBSP-b1.xml
--- beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/beast1/testEBSP-b1.xml	1970-01-01 00:00:00.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/beast1/testEBSP-b1.xml	2022-04-04 07:18:36.000000000 +0000
@@ -0,0 +1,661 @@
+<?xml version="1.0" standalone="yes"?>
+
+<!-- Generated by BEAUTi v1.10.4 Prerelease #bc6cbd9                         -->
+<!-- Modified to v1.7.0 -->
+<beast version="1.10.4">
+	
+
+	<!-- The list of taxa to be analysed (can also include dates/ages).          -->
+	<!-- ntax=63                                                                 -->
+	<taxa id="taxa">
+		<taxon id="AF271887i_3405"/>
+		<taxon id="AF271886i_3319"/>
+		<taxon id="AF271885i_3289"/>
+		<taxon id="AF271884i_2659"/>
+		<taxon id="AF271883i_2432"/>
+		<taxon id="AF271882i_2153"/>
+		<taxon id="AF271881i_2116"/>
+		<taxon id="AF271880i_2115"/>
+		<taxon id="AF271879i_2113"/>
+		<taxon id="AF271878i_2000"/>
+		<taxon id="AF271877i_1999"/>
+		<taxon id="AF271876i_1797"/>
+		<taxon id="AF271875i_1380"/>
+		<taxon id="AF271874i_1359"/>
+		<taxon id="AF271873i_4055"/>
+		<taxon id="AF271872i_4053"/>
+		<taxon id="AF271871i_4036"/>
+		<taxon id="AF271870i_4033"/>
+		<taxon id="AF271869i_4020"/>
+		<taxon id="AF271868i_3471"/>
+		<taxon id="AF271867i_3468"/>
+		<taxon id="AF271866i_3465"/>
+		<taxon id="AF271865i_3463"/>
+		<taxon id="AF271864i_3461"/>
+		<taxon id="AF271863i_3460"/>
+		<taxon id="AF271862i_3458"/>
+		<taxon id="AF271861i_3452"/>
+		<taxon id="AF271860i_3400"/>
+		<taxon id="AF271859i_3393"/>
+		<taxon id="AF271858i_3318"/>
+		<taxon id="AF271857i_2957"/>
+		<taxon id="AF271856i_2926"/>
+		<taxon id="AF271855i_2862"/>
+		<taxon id="AF271854i_2856"/>
+		<taxon id="AF271853i_2852"/>
+		<taxon id="AF271852i_2685"/>
+		<taxon id="AF271851i_2681"/>
+		<taxon id="AF271850i_2673"/>
+		<taxon id="AF271849i_2663"/>
+		<taxon id="AF271848i_2446"/>
+		<taxon id="AF271847i_2438"/>
+		<taxon id="AF271846i_2429"/>
+		<taxon id="AF271845i_2386"/>
+		<taxon id="AF271844i_2150"/>
+		<taxon id="AF271843i_2147"/>
+		<taxon id="AF271842i_2141"/>
+		<taxon id="AF271841i_2134"/>
+		<taxon id="AF271840i_2130"/>
+		<taxon id="AF271839i_1997"/>
+		<taxon id="AF271838i_1803"/>
+		<taxon id="AF271837i_1801"/>
+		<taxon id="AF271836i_1796"/>
+		<taxon id="AF271835i_1767"/>
+		<taxon id="AF271834i_1339"/>
+		<taxon id="AF271833i_1240"/>
+		<taxon id="AF271832i_1226"/>
+		<taxon id="AF271831i_1164"/>
+		<taxon id="AF271830i_1150"/>
+		<taxon id="AF271829i_0923"/>
+		<taxon id="AF271828i_0922"/>
+		<taxon id="AF271827i_0883"/>
+		<taxon id="AF271826i_0873"/>
+		<taxon id="AF271825i_0800"/>
+	</taxa>
+	
+	
+
+	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
+	<!-- ntax=63 nchar=411                                                       -->
+	<alignment id="alignment" dataType="nucleotide">
+		<sequence>
+			<taxon idref="AF271887i_3405"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACCGTCCCTGCCTCGGCCATACACTATCGCAATGCTTCGGATGTCTACCACGTCACCAATGACTGTCCGAATTCCAGCATAGTCTATGAGTCTGAAAACCACATCCTACACCTTCCGGGGTGTGTGCCCTGTGTGAGGATTGGGAACGTGTCACAATGCTGGGTGGCCCTAACCCCCACCGTGGCGGCGCCGTACCTCAATGCTCCGGTCGACTCCCTACGGAGGCACGTGGACCTGATGGTTGGCGCCGCTACTATGTGCTCAGCATTTTATGTTGGGGACCTGTGCGGGGCTGTGTTCCTGGCGGGCCAGTTGGTGACGTTTCGACCGCGACGCCACTGGACCACTCAAGATTGTAACTGTTCCATCTATGCCGGGCACATCACA
+		</sequence>
+		<sequence>
+			<taxon idref="AF271886i_3319"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACCGTTCCTGCATCAGCCATCCACTATCGCAACAGCTCGGGCGTCTACCACATCACCAATGACTGCCCCAATTCCAGCATAGTGTACGAGACTGACCATCACATCCTACACCTCCCAGGATGCGTGCCCTGTGTGAGGAGCGGGAACGAGTCGCGATGCTGGGTGTCCTTAACCCCCACCGTGGCAGCGCCGTACCAAAATGCACCACTTCAGTCCTTGCGACGGCATGTAGACCTGATGGTGGGCGCTGCTACCATGTGTTCTGCCCTTTATATCGGCGACTTGTGTGGGGGCTTGTTTTTGATAGGCCAGGCTTTTACTTTCCAACCACGCCGCCATTGGACTACTCAGGATTGCAATTGCTCCATCTACTCAGGCCACATCACA
+		</sequence>
+		<sequence>
+			<taxon idref="AF271885i_3289"/>
+			CTTTTGGCACTTCTCTCGTGCCTGACCGTTCCCGCATCAGCCATTCACTATCGCAACAGCTCGGGCATCTACCACATCACCAATGACTGCCCCAACTCCAGCATAATTTATGAGGCTGACCATCACATCCTACACCTCCCAGGATGCGTGCCCTGTGTGAGGAGCGGGAACGTGTCGCGATGCTGGGTGTCCTTGACCCCCACCGTGGCAGCGCCGCACCTCAACGCACCACTTCGGTCCTTGCGACGGCATGTGGATCTGATGGTGGGCGCCGCTACTATGTGTTCTGCCTTTTACATCGGCGACTTGTGTGGGGGTTTGTTTCTGATAGGCCAGGCCTTTACTTTCCAACCACGCCGCCACTGGACTACCCAGGATTGCAATTGCTCCATCTACTCAGGCCACATTACA
+		</sequence>
+		<sequence>
+			<taxon idref="AF271884i_2659"/>
+			CTTTTGGCACTTCTCTCGTGCCTGACCGTTCCTGCATCAGCCATTCACTATCGCAACAGTTCGGGCGTCTACCACGTCACCAATGACTGCCCCAATTCCAGCATAGTTTATGAGGCTGACCATCACATCCTACACCTCCCAGGATGCGTGCCCTGTGTGAGGAGCGGGAACGTGTCGCGATGCTGGGTGTCCTTAACCCCCACCGTGGCGGCGCCATACCTCAATGCGCCACTTCAGTCCTTGCGACGGCATGTGGACCTGATGGTGGGCGCTGCTACCATGTGTTCTGCCCTTTACATCGGCGACTTGTGTGGGGGCCTGTTTCTGATAGGCCAGGCCTTTACTTTCCAACCACGCCGCCACTGGACTACTCAGGATTGCAATTGCTCCATCTATTCAGGCCACATCACA
+		</sequence>
+		<sequence>
+			<taxon idref="AF271883i_2432"/>
+			CTTTTGGCACTTCTTTCGTGCCTGACCGTTCCTGCATCAGCCACTCACTATCGCAATAGTTCGGGTGTCTACCACATCACTAATGACTGCCCGAATTCCAGCATAGTTTATGAGGCTGACCATCACATCTTACACCTCCCAGGATGCTTGCCCTGTGTGAAGAGCGGGAACGTGTCGCGATGCTGGGTGTCCTTAACCCCCACCGTGGCAGCGCCGCATCATAACGCACCACTTRAGTCCTTGCGACGGCATGTGGACCTGATGGTGGGCGCTGCTACCATGTGTTCTGCCCTCTACATCGGCGACTTGTGCGGGGGCTTGTTTCTGATAGGCCAGGCCTTTASTTTCCAACCGCGCCGCCACTGGACTACTCAGGATTGTAATTGCTCCATCTATACAGGCCACATTACA
+		</sequence>
+		<sequence>
+			<taxon idref="AF271882i_2153"/>
+			CTTCTGGCACTCCTCTCGTGCCTGACCGTCCCCGCATCGGCCATACACTATCATAACACCTCGGGCATCTACCACATCACCAATGATTGCCCAAATTCCAGCATAGTCTATGAGTCCGATCATCACATAATGCACCTTCCGGGGTGCGTGCCATGTGTGATGGAAGGGAACAGATCCAGGTGTTGGGTGGCCCTGTCTCCCACAGTGGCGACCTCACACGTTGGTGCTCCAGTTGAGTCCATGCGACGACATGTGGACCTGATGGTGGGCGCTGCCACTTTGTGCTCCGCCCTATACGTCGGGGACTTGTGCGGAGGTGTGTTTCTGGTTGGTCAGATGTTCACCTTTCAGCCTCGTCGCCACTGGACTACCCAGGACTGCAACTGCTCAATCTATTCTGGGCATGTCACG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271881i_2116"/>
+			CTCTTGGCACTCCTTTCATGCCTGACCGTTCCCGCCTCGGCCATACACTATCGCAATGCTTCGGACGTCTACCACATCACCAACGACTGTCCGAATTCCAGCATAGTCTATGAATCCGAGAATCACATCTTACACCTTCCGGGGTGCGTACCCTGTGTGAAGGTCGGGAATAGGTCACAATGCTGGGTGGCCCTAACCCCCACCGTGGCGGCGTCGTACCTCAATGCTCCAATCGACTCCTTACGGAAGCACGTGGACCTGATGGTTGGCGCCGCTACTGTGTGCTCAGCTCTCTATGTTGGAAACGTGTGCGGGGCTGTGTTCCTGGCGGGCCAGATGGTGACGTTTCGACCGCGGCGCCACTGGACCACTCAGGAGTGCAACTGTTCCATCTATGCTGGGCACCTCACA
+		</sequence>
+		<sequence>
+			<taxon idref="AF271880i_2115"/>
+			CTCTTGGCACTCCTTTCATGCCTGACCGTTCCCGCCTCGGCCATACACTATCGCAATGCTTCGGACGTCTACCACATCACCAACGACTGTCCGAATTCCAGCATAGTCTATGAATCCGAGAATCACATCTTACACCTTCCGGGGTGCGTACCCTGTGTGAAGGTCGGGAATAGGTCACAATGCTGGGTGGCCCTAACCCCCACCGTGGCGGCGTCGTACCTCAATGCTCCAATCGACTCCTTACGGAAGCACGTGGACCTGATGGTTGGCGCCGCTACTGTGTGCTCAGCTCTCTATGTTGGAGACGTGTGCGGGGCTGTGTTCCTGGCGGGCCAGATGGTGACGTTTCGACCGCGGCGCCACTGGACCACTCAGGAGTGCAACTGTTCCATCTATGCTGGGCACGTCACA
+		</sequence>
+		<sequence>
+			<taxon idref="AF271879i_2113"/>
+			CTTTTGGCACTTCTCTCGTGCCTGACCGTCCCCACGTCGGCCATACACTATCATAACACCTCGGGCATCTATCACATCACCAACGATTGCCCAAATTCCAGCATAGTTTATGAGTCCGACTACCACATAGTGCACCTTCCGGGGTGCGTACCATGTGTGAGAACCGGAAACGCGTCGACGTGTTGGGTGGCCTTGTCTCCCACAGTGGCGGCCCCATACATCGGTGCTCCAGTTGAGTCTCTACGGCGACACGTGGACCTGATGGTGGGAGCTGCCACCTTGTGCTCTGCCCTATATGTCGGGGACCTGTGCGGAGGTGCGTTTCTGGTCGGCCAGATGTTCACCTTCCGCCCTCGTCTCCACTGGACCACCCAGGACTGCAACTGTTCAATCTACTCTGGGCATATCACG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271878i_2000"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACCGTCCCCGCATCGGCCATACACTATCATAACACCTCGGGCATCTATCACATCACCAATGATTGCCCAAATTCCAGCATAGTTTATGAGTCCAGCAACCACATAATGCACCTTCCGGGGTGTGTACCATGTGTGAGGAGCGGGAACGTGTCGAGCTGTTGGGTGGCTTTAACTCCCACAGTGGCGGCCCCATACGTCGGTGCTCCAGTTGAGTCTCTACGACGACACGTGGACCTGATGGTGGGTGCTGCCACTTTGTGCTCCGCCCTATATGTCGGGGACCTGTGCGGAGGTGTGTTTCTGGTGGGTCAGATGTTCACCTTCCGCCCCCGCCTCCACTGGACTACTCAAGACTGTAACTGTTCAATCTATTCTGGGCATGTCACG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271877i_1999"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACCGTCCCCGCATCGGCCATACACTATCATAACACCTCGGGCATCTATCACATCACCAATGATTGCCCAAATTCCAGCATAGTTTATGAGTCCAGCAACCACATAATGCACCTTCCGGGGTGTGTACCATGTGTGAGGAGCGGGAACGTGTCGAGGTGTTGGGTGGCTTTAACTCCCACAGTGGCGGCCCCATACGTCGGTGCTCCAGTTGAGTCTCTACGACGACATGTGGACCTGATGGTGGGTGCTGCCACTTTGTGCTCCGCCCTATATGTCGGGGACCTGTGCGGAGGTGTGTTTCTGGTGGGTCAGATGTTCACCTTCCGCCCCCGCCTCCACTGAACTACTCAAGACTGTAACTGTTCAATCTATTCTGGGCATGTCACG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271876i_1797"/>
+			CTCTTGGCACTCCTCTCGTGCCTGACTGTCCCCGCATCAGCCACGCATTATCGCAATGCTTCGGGCGTCTACCACATCACCAACGACTGCCCGAATTCCAGCATAGTGTACGAGGGTCAGCATCACATCCTGCACCTTCCCGGGTGTGTACCCTGTGTCAAAACCGACAACGTATCGCGGTGTTGGGTAGCTTTGACCCCCACTGTGGCGGCTCCCTACCTCAATGCTCCAACAGAAGAGCTCAGGCACCATGTGGACATGCTGGTGGGTGCCGCTACTTTTTGCTCCGCCCTTTACATCGGCGACTTGTGTGGGGGAGCCTTCTTAGTGGGCCAGCTATTCACATTCCGGCCGCGTCGCCATTGGACCACGCAGGATTGCAACTGTTCCATCTACGCTGGTCACATCACA
+		</sequence>
+		<sequence>
+			<taxon idref="AF271875i_1380"/>
+			CTCTTGGCACTCCTCTCGTGCCTGACTGTCCCCGCATCGGCCGCACATTATCGCAATGCTTCGGGTGTCTACCATATCACCAATGACTGCCCGAATTCTAGCATAGTGTACGAGGCTGATCACCACATCATGCACCTTCCGGGGTGCGTGCCCTGCGTCAAGACCGGCAACGTATCGCGGTGTTGGGTAGCTTTGACCCCCACTGTGGCGGCCCCCTACCTCAATGCTCCAACAGAAGCGCTTAGGCGCCATGTGGACTTGATGGTGGGTGCCGCCACTTTCTGCTCCGCCCTTTACATCGGCGATTTGTGTGGGGGAGCCTTCTTAGTGGGCCAACTATTCACATTCCGGCCGCGTCGCCATTGGACCACGCAGGACTGCAACTGCTCCATCTACACCGGTCACATCACA
+		</sequence>
+		<sequence>
+			<taxon idref="AF271874i_1359"/>
+			CTTTTGGCACTTCTCTCGTGCCTGACTGTTCCTGCATCAGCCATTCACTATCGCAACAGTTCGGGCATCTACCACATCACCAACGATTGCCCAAATTCTAGCATAGTTTATGATTCTGACCATCACATCCTACACCTCCCAGGATGCGTACCCTGTGTGAGGAGCGGGAACATGTCGCGATGCTGGGTGTCCTTAACCCCCACCGTGGCAGCGCCGTATCCCAACGCACCACTTCAGTCCTTGCGACGGCATGTAGACCTGATGGTGGGCGCTGCTACCATGTGTTCAGCCTTCTACGTCGGCGACCTGTGTGGGGGCCTATTTTTGATAGGCCAGGCCTTTAATTTCCAACCACGCCGCCACTGGACTACTCAGGATTGCAATTGCTCCATCTATACAGGCCACATCACA
+		</sequence>
+		<sequence>
+			<taxon idref="AF271873i_4055"/>
+			CTCTCGGCACTTCTCTCGTGCTTGACTGTCCCCGCTTCGGCCGTCAACTATCGCAACATCTCGGGCGTCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTCCCAGGTTGTGTGCCCTGCGTGAGAGTGGGGAATCAGTCGCGTTGCTGGGTGGCCCTTACCCCTACCGTCGCAGCGCCATACATTGGCGCGCCGCTTGACTCCCTGCGGAGTCACGTGGATCTGATGGTGGGAGCAGCCACTGTTTGCTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCGCCTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACTACCCAGGATCGCAATTGTCCCATCTACACTGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271872i_4053"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTTCCCGCTTCGGCCATCAACTACCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGCCCAAATTCAAGCATAGTATATGAGGCCGACCATCACATCCTGCACCTTCCGGGTTGTGTGCCCTGTGTGAGGGAGGGGAATCAGTCGCGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCCTGCGGAGTCACGTGGATCTGATGGTGGGAGCCGCTACTGTTTGCTCACCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTTGGTCAAATGTTCTCTTTCCGACCACGGCGTCACTGGACTACTCAGGAATGCAATTGTTCCATCTACGCGGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271871i_4036"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGCCCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGAGAATCAGTCTCGCTGCTGGGTGGCCCTCACTCCTACCGTCGCAGCGCCATATATCGGCGCGCCGCTTGATTCCCTGCGGAGTCATGTGGATCTGATGGTGGGAGCTGCCACTGCTTGTTCGGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAAATTTTTCCTTTCAGACCACGGCGCCACTGGAATACCCAGGAATTGCATTGTTCCATCTATACAGGGCACATCACG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271870i_4033"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCCTCGGCCACTAATTACCGCAATGCTTCGGGTGTCTACCACGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCATCTTCCAGGCTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCCACCGTCGCGACGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCTTCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271869i_4020"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGCCCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGAGAATCAGTCTCGCTGCTGGGTGGCCCTCACTCCTACCGTCGCAGCGCCATATATCGGCGCGCCGCTTGATTCCCTGCGGAGTCATGTGGATCTGATGGTGGGAGCTGCCACTGCTTGTTCGGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTTTCTTTCAGACCACGGCGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271868i_3471"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCACTTCGGCTATCAGCTATCGCAATGTCTCGGGCATTTATCACATCACCAACGACTGCCCGAATTCAAGCATAGTATATGAGGCCGACCATCACATCTTGCACTTTCCAGGTTGCGTGCCCTGTGTGAGAGAGGGGAATCAGTCGCGTTGCTGGGTGGCCCTTACCCCTACCGTCGCAGCGCCATACATCGGCGCGCCACTTGAGTCCCTACGGGGTCATGTGGATTTGATGGTGGGGACCGCCACTRTTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTATTCCTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACCACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACC
+		</sequence>
+		<sequence>
+			<taxon idref="AF271867i_3468"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCTATCAACTACCATAATGCCTCGGGCATCTACCATGTCACCAAYGATTGCCCGAATGCAAGCATAGTGTATGAGGCCGACCACCACATCTTGCACCTTCCAGGTTGCTTGCCCTGTGTGAGAGTGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACCCCTACCGTTGCAGCGCCATACATCGGCGCACCGCTTGAGTCCTTGCGGAGTCATGTGGATCTAATGGTGGGGGCTGCCACTGCYTGTTCAGCCCTCTACATCGGAGACTTGTGCGGCGGCCTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCGCGACGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATTACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271866i_3465"/>
+			CTCTTGGCACTTCTCTCGTGCTTGACTGTCCCCGCTTCGGCCACCAACTATCGCAACGCTTCGGGCGTCTACCATGTCACCAATGACTGCCCGAACTCAAGCATAGTGTATGAGGCCGACTATCACATCCTACACCTCCCAGGTTGTGTGCCTTGTGTGAAAACAGGGAACCAGTCACGTTGTTGGGTGGCCCTTACTCCTACTGTCGCAGCGCCATACATCGGTGCGCCGCTTGAGTCCTTACGGAGTCATGTGGATCTGATGGTGGGGGCAGCCGCCGCTTGTTCAGCCCTTTATGTCGGGGACCTGTGCGGCGGCGTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGTCACTGGACTACCCAGGATTGCAATTGTTCTATCTACACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271865i_3463"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCCTCGGCCGTTAACTACCACAATGTCTCGGGCATTTACCACGTCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCACCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGGGTGGGGAATCAATCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACGTTGGCGCGCCACTTGAGTCTTTGCGGAGTCATGTGGATTTGATGGTGGGGGCTGCCACTGTTTGCTCAGCCCTTTACATCGGGGATTTATGCGGTGGTTTGTTCCTGGTCGGTCAGATGTTTTCTTTCCGGCCACGGCGCCACTGGACCACCCAGGATTGCAACTGTTCCATCTATACAGGGCACATCATG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271864i_3461"/>
+			CTCTTGGCACTTCTTTCGTGCCTGACTGTCCCCGCTTCGGCCACCAATTACCGCAATGCCTCGGGCATCTACCATGTTACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCATATCTTNCACCTTCCAGGTTGCGTGCCCTGTGTGAGAGTGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACCCCTACCGTCGCAGCGCCATACATCGGCGCGCCACTTGAGTCCTTGCGGAGTCATGTGGACCTGATGGTGGGGACTGCCACTGTTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTTTTGGTTGGTCAGATGTTCTCTTTCCGACCGCGGCGCCACTGGACCACCCAGGATTGCAATTGTTCCATCTATACAGGACACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271863i_3460"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCACCTCGGCCATCAACTATCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGTCCGAACTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCATCTCCCAGGWTGCGTGCCCTGTGTGAGAGTGGGGAATGTGTCAAGMTGTTGGGTGGCCCTTACCCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCTCTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATTTATGTGGCGGCTTGTTTTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271862i_3458"/>
+			CTCTTGGCACTTCTTTCGTGCCTGACTGTCCCCGCTTCGGCCACCAACTACCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCCTGCACCTTCCAGGTTGCGTGCCTTGCGTGAGGGTGGGGAATCAGTCACGTTGCTGGGTGGCTCTTACCCCTACTGTCGCAGCGCCACACATCGGCGCGCCACTTGAGTCCTTGCGGAGTCATGTGGACTTGATGGTGGGGACTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGTGGCTTGTTTTTGGTTGGTCAGATGTTCTCTTTCCGACCGCGGCGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTACACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271861i_3452"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCCTCGGCCACTAATTACCGCAATGCTTCGGGTGTCTACCACGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCATCTTCCAGGCTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGWTGCTGGGTGGCCCTTACTCCCACCGTCGCGACGCCATACATCGGCGCACCGSTTGAGTCCCTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGYTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGWTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCTTCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271860i_3400"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATCGCAATGCTTCGGGTATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTACGAGGCCGACCACCACATTTTACACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGAGTCATGTGGATTTGATGGTGGGGGCTGCCACTGTCTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGTGTGTTCTTGGTCGGTCAGATGTTTTCTTTCCGACCACGACGCCACTGGACTACCCAGGATTGCAATTGCTCCATCTATACAGGGCACATCATG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271859i_3393"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTACCGCAATGCTTCGGGCATCTACCATATCACCAATGATTGCCCGAATTCAAGCATAGTGTATGAGGCCGATCACCACATCTTGCACCTTCCAGGCTGCGTGCCCTGCGTGAGATCGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCGGCGCCACACATCGGCGCRCCGCTTGAGTCCTTGCGGAGTCAYGTGGATCTGATGGTGGGAACTGCCACTGTTTGTTCAGCCCTTTACATCGGCGATTTGTGTGGYGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCGCGGCGCCACTGGACTACCCAGGATTGCAACTGTTCCATCTATACAGGGCACATYACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271858i_3318"/>
+			CTCTTGGCACTTCTCTCATGCCTGACTGTCCCTGCTTCGGCTATTAACTATCGCAATGYTTCGGGCATTTACCAYGTCACCAATGACTGTCCGAATTCTAGCATAGTGTATGAGGCCGATCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAAGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCATCGCAGCGCCATTCATCGGCGCGCCGCTTGAGTCTCTGMGGAGTCATGTGGAYTTGATGGTGGGGGCTGCYACTGCTTGTTCGGCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACKACCCAGGACTGTAAYTGKTCCATCTATACAGGGCACATTACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271857i_2957"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCRTCAACTACCGCAAYGTCTCGGGCATCTACCATGTCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCAYCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAAACAGGGGAATCAGTCACGTTGCTGGGTGGCCCTCACYCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCCTGCGGAGTCATGTGGATTTRATGGTGGGAGCTGCCACTGTTTGTTCAGCCTTTTACATCGGCGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTCTCMTTCCGACCACGGCGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCATG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271856i_2926"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTATCGCAATGTTTCGGGCGTCTACCACGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGAGCATCACATCTTGCACCTCCCAGGTTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCAAGTTGCTGGATGGCCCTTACCCCTACTGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCTTGCGGAGTCATGTGGATCTGATGGTGGGGGCCGCCACTGTTTGTTCAGCCCTTTACATCGGCGATCTGTGTGGCGGCTTGTTCTTGGTTGGCCAAATGTTCTCTTTCCAACCGCGGCGCCACTGGACCACCCAGGAGTGCAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271855i_2862"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCYATCAACTACCGCAATGCYTCGGGCGTCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCAYATCTTGCACCTTCCAGGATGCGTGCCCTGCGTGAAAGTGGGAAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATATRTTGGCGCGCCGCTTGAGTCCYTGCGGAGTCATGTGGACCTGATGGTGGGAGCTGCTACTGTCTGCTCAGCCCTTTACATTGGGGATTTGTGTGGCGGCGTGTTCTTGGTCGGCCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACTACCCAGGAGTGCAATTGTTCCATCTATACAGGGCAACTTACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271854i_2856"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCTGCTTCGGCCATCAATTACCGCAATGCCTCGGGCGTTTACCACATCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCATCTTCCAGGTTGCGTGCCCTGCGTAAGAGTGGGGAATCAGTCACGCTGCTGGGTGTCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCACCACTTGAGTCTCTACGGAGTCATGTAGACTTGATGGTGGGAGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTTCTGGTCGGTCAGATGTTCTCTTTCCGACCGCGACGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271853i_2852"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTACCACAATGTCTCGGGCATCTACCATGTCACCAATGATTGCCCGAACTCAAGCATAGTGTATGAGGCCGAGCACCACATCCTGCACCTTCCTGGTTGCGTGCCCTGCGTGAGAGTGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGACTCCTTGCGGAGTCATGTGGATTTGATGGTGGGAACCGCCACTGTTTGTTCAGCTCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTTTCTTTTCAACCACGGCGCCATTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGACACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271852i_2685"/>
+			CTCTTGGCACTTCTCTCGTGCTTGACTGTCCCCGCTTCGGCCATTAACTACCGCAATGCGTCGGGCATCTACCATGTCACCAATGATTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGTGTGAGAGTGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCCACCGTCGCAGCGCCATACATCGGCGCGTCACTTGCATCTTTGCGGAGTCATGTGGATCTGATGGTGGGGACCGCCACTGTTTGTTCAGCCCTCTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCAACCACGGCGCCACTGGACTACCCAGGATTGCAATTGTTCTATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271851i_2681"/>
+			CTCTTGSCACTTCTCTCGTGCCTGACTGTCCCCACTTCGGCCATTAACTACCATAATGTTTCGGGCATCTATCACGTCACCAATGATTGTCCGAATTCAAGCATTGTGTATGAGGCCGATCATCACATCTTGCACGTTCCAGGCTGTGTGCCCTGCGTGAGAGAGGGAAATCAGTCACGTTGCTGGGTGGCCATTACTCCTACCCTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCCTGCGGAGTCACGTGGATMTGATGGTGGGGGCTGCCACTGCTTGNTCAGCCCTTTACATCGGGGATTTGTGTGCCGGTCTGTTCTTGGTTGGTCAGATGTTATCTTTCCGACCACGGCGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGAGCGNGTGTT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271850i_2673"/>
+			CTTTTGGCACTTCTCTCGTGCCTGACCGTCCCCGCTTCGGCCACCAACTATCGCAATGTCTCGGGCGTCTACCACATCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAAAGAGGGGAACCGGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACCTTGGCGCGCCACTTGAGTCTTTACGGAGCCATGTGGACTTGATGGTGGGAGCTGCCACTGCTTGTTCAGCCCTTTACATCGGAGACTTGTGTGGTGGCTTGTTCCTGGTTGGTCAGATGTTCTCTTTCCGACCACGACGCCACTGGACTACCCAAGAATGCAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271849i_2663"/>
+			CTCTTAGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCGTTAACTACCGCAATGCTTCGGGTGTCTATCATATCACCAATGATTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCATGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGGGAACCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCATYGCAGCGCCATACATCGGCGCGTCGCTCGAGTCCTTGCGGAGTCATGTGGATGTGATGGTGGGGGCYGCCACTGTTTGTTCAGCCCTTTACATCGGGGACTTGTGTGGTGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCRCGGCGCCACTGGACTACCCAGGACTGCAACTGTTCCATTTATACAGGGCAGATACTG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271848i_2446"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATCGCAATGCCTCGGGCATCTATCACGTCACCAATGACTGCCCGAATTCGAGCATAGTGTATGAGGCCGACAACCACATCCTGCACCTTCCAGGTTGCGTGCCCTGTGTGAAAGAGGGGAATCAGTCACGTTGCTGGGTGTCCCTTACTCCCACCGTCGCAGCGCCATACATCGGCGCGCCACTTGCGTCTCTACGGAGTCACGTGGATTTGATGGTGGGGGCTGCCACTGTTTGTTCAGCCCTCTACATCGGGGACTTGTGCGGCGGCTTGTTCTTGGTTGGCCAGATGTTCTCTTTCCAACCACGGCGTCACTGGACCACCCAGGATTGTAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271847i_2438"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCTGTCAACTACCGCAAYGCTTCGGGCGTTTACCATATCACCAATGAYTGTCCGAATGGAAGCATAGTGTATGAGGCCGACCATCACATYTTGCACCTCCCAGGTTGCGTGCCCTGCGTGAGARAGGGGAATCAGTCACGTTGCTGGGTAGCCCTTACTCCTACCMTCGCGGCGCCACACATCGGCGCGCCACTTGAATCTCTACGGAAACATGTGGATTTGAKGGTGGGAGCTGCTACWGCCTGTTCAGCCCTTTACATCGGGGATTTGTGTGCCGGCTTGTTCTTGGTCGGTCAGATGTTATCATTCCGACCACGACGCCACTGGACTACCCAGGATTGCAGTTGTTCCATCTAAACAGGACGAAGTGTT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271846i_2429"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTACCGCAATGTCTCGGGCATTTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGTTGCTGGGTGGCCCTAACTCCTACCGTCGCGGCACCACACATCGGTGCGCCACTTGAGTCTCTACGGAGTCATGTGGATTTGATGGTGGGGACCGCCACTGTTTGTTCAGCCCTTTACATCGGGGATTTATGTGGTGGTTTGTTCCTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGTCACTGGACCACCCAGGATTGCAATTGTTCCATCTACACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271845i_2386"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTACCGCAATGCTTCGGGCGTTTACCACATCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCATGCACCTTCCAGGTTGCGTGCCCTGCGTGAGGACGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGTGCCGTATATTGGCGCGCCACTTGACTCTCTTCGGAGTCATGTGGATTTGATGGTGGGGGCTGCTGCTGCTTGTTCAGCCCTTTACGTCGGGGACTTGTGTGGTGGCGTGTTCCTGGTCGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACTACCCAGGACTGCAACTGTTCCATCTACACAGGGCACATTACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271844i_2150"/>
+			CTCTTGGCACTTCTCTCGTGCCTGAGTGTCCCCGCCTCGGCAATTAATTACCGCAATGCTTCGGGTGTCTACCACGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCATCTTCCAGGCTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCCACCGTCGCGACGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGATTCATGTGGATCTGATGGTGGGGGCTGCCATTGCTTGTTCACCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTCGGTCAGATGTTCTCTTCCCGACCAAGGCTTCACTGGACTACTCAGGATCGCCATTGTTCCATCTATACGGGGCACATCTCC
+		</sequence>
+		<sequence>
+			<taxon idref="AF271843i_2147"/>
+			CTCTTGGCACTCCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTATCACAACACCTCGGGCGTCTACCACGTCACCAATGACTGCCCGAATTCAAGCATAGTCTATGAGGCCGACCATCACATCTTGCATCTCCCAGGGTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCACGTTGCTGGGTGGCCCTCACCCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCTTGCGGAGTCACGTGGATCTGATGGTGGGGGCAGCTACTGTCTGCTCTGCCCTTTACATCGGGGATTTGTGTGGCGGCGTGTTCTTGGTTGGTCAGATGTCCTCTTTCCGACCACGGCGCCACTGGACTACCCAGGAGTGCAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271842i_2141"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCACTAACTACCGCAACGCTTCGGGCATCTACCATGTCACCAATGACTGCCCGAATGCGAGCATAGTGTATGAGGCCGACCATCACATCCTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAAAGGGGAATCAGTCAAGCTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCTTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGTCTGTTCAGCCCTCTACATCGGGGATTTGTGTGGCGGCGTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGACGCCACTGGACTACCCAGGATTGCAATTGTCCCATCTATACAGGGCCCATTACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271841i_2134"/>
+			CTTCTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATAGCAACGTCTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGACCGAACATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGCGTGACGGGAATCAGTCGCGTTGCTGGGTGGCCCTTACCCCTACCGTCGCAGCGTCACGACTCGACGCGCCGCTTGAGTCCTTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGCTTGCTCAGCCCTTTACATCGGGGATTTGTGTGGCGGTCTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGCCCACGGCGCCTCTGGACTACCCAGGATTGCAATTGTTCCATTTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271840i_2130"/>
+			CTTTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTATCGCAATGTCTCGGGCATCTACCACGTCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGGACGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCACTTGAGTCTCTACGGAGTCATGTGGATTTGATGGTGGGGGCTGCCACTGTTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCCTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACCACCCAGGATTGCAATTGTTCCATCTATACGGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271839i_1997"/>
+			CTCTTGGCACTTCTTTCGTGCCTGACTGTTCCCNCTTCGGCCACTAACTATCGCAATGTTTCGGGCATCTACCATGTTACCAACGACTGCCCGAATTCAAGCATAGTATATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGYGTGAAAGTCGGGAACCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGYGCTCCGCTTGAGTCCCTGCGGAATCATGTGGATYTGATGGTGGGGGCTGCCACTGTTTGTTCAGCCCTTTACATCGGRGAYTTGTGTGGCGGCTTGTTTTTGGTTGGTCAGATGTTTTCTTTTCGGCCACGACGCCACTGGACTACCCAAGACTGCAACTGTTCCATCTATACGGGACACATCATG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271838i_1803"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCACCAACTATCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGATCACCACATCTTGCACTTGCCAGGTTGCGTGCCCTGCGTGCAAACGGGGAATCAGTCACGTTGCTGGGTGGCCCTCACTCCTACCGTCGCAGCGCCGTATATCGGCGCGCCACTTGAGTCTTTACGGAGTCATGTGGATTTGATGGTGGGAGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGACTTGTGTGGCGGCCTGTTCCTGGTTGGTCAGATGTTCTCTTTCCGACCGCGGCGCCACTGGACCACCCAAGACTGCAATTGTTCCATCTACACAGGGCACATTACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271837i_1801"/>
+			CTCTTGGCACTTCTCTCTTGTCTGACTGTCCCCGCTTCGGCCACTAACTACCGCAATGTTTCGGGCATCTACCACGTCACCAATGACTGCCCGAACTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGTGTGAGGACGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACCCCTACCGTCGCATCGCCATACATCGGCGCGCCACTTGCATCTCTACGGACTCATGTGGACTTGATGGTGGGGGCCGCCACTGTTTGTTCAGCCCTTTACATCGGAGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAAATGTTCTCTTTCCGACCAAGGCGCCACTGGACCACCCAGGATTGCAACTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271836i_1796"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCTTCAACTACCGCAACATCTCGGGTATTTACCATGTCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATTTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGGGAGGGGAATCAGTCGCGCTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGAGTCACGTGGATATGATGGTGGGGGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATCTGTGTGGCGGCTTGTTTCTGGTTGGTCAGATGTTTTCTTTCCGACCACGACGCCACTGGACTACCCAGGAGTGCAATTGTTCCATCTATTCAGGGCATATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271835i_1767"/>
+			CTCTTGGCACTTCTTTCGTGCTTGACTGTCCCCGCTTCGGCCGTTAACTACCGCAATGTCTCGGGCATCTACTATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCACCACATCTTGCACTTGCCAGGCTGCGTGCCCTGCGTGCGGGTGGGGAACCAGTCACGTTGCTGGGTGGCTCTCACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCACTTGAGTCTTTACGGAGTCATGTGGATTTGATGGTGGGGGCTGCCACTGTTTGTTCAGCCCTCTACATCGGGGATTTGTGTGGTGGCCTGTTCCTGGTTGGTCAGATGTTTTCTTTCCAACCACGGCGCCACTGGACCACCCAAGACTGCAATTGTTCCATCTATACGGGGCATATTACC
+		</sequence>
+		<sequence>
+			<taxon idref="AF271834i_1339"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTTCCCGCTTCGGCCGTTAACTACCGCGATGCTTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCCTGCATCTCCCGGGTTGCGTGCCCTGCGTGAGAGTTGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCATCGCATCGCCATACATCGGTGCGCCGCTTGAATCCCTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGTTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGTCACTGGACCACCCAGGATTGCAATTGTTCCATCTACACGGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271833i_1240"/>
+			CTCTTGGCACTACTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAATTACCGCAATGCCTCGGGCGTCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCCTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGCTGCTGGGTGGCCCTTACTCCTACTGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCTTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTTTTGGCTGGTCAGATGTTTTCTTTCCGGCCACGGCTCCACTGGACCACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271832i_1226"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCTTCAACTACCGCAACATCTCGGGTATTTACCATGTCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATTTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGGGAGGGGAATCAGTCACGCTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGAGTCATGTGGATATGATGGTGGGGGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATCTGTGTGGCGGCTTGTTTTTGGTTGGTCAGATGTTTTCTTTCCGACCACGACGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATGCAGGGCATATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271831i_1164"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATCGCAATGCCTCGGGCATCTACCATGTCACCAATGATTGCCCGAATTCAAGCATAGTGTATGAGGCCGAATATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGCGATGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTTGCAGCGCCGTACGTTGGCGCGCCGCTTGAGTCCCTGCGGAGTCATGTGGATCTGATGGTGGGAGCTGCCACTGTTTGTTCAGCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTTGGTCAAATGTTCTCTTTCCAGCCACGGCGTCACTGGACTACCCAGGGTTGTAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271830i_1150"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCACTAACTATCGCAATGTCTCGGGTATCTATCATGTCACCAATGATTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGCTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGCCTCCCTGCGGAGTCATGTGGATCTGATGGTGGGGGCCGCCACTGCTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATTTTCACCTTCCGACCACGGCGCCACTGGACTACCCAGGAATGCAATTGTTCCATCTATACAGGGCACATCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271829i_0923"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCACCAACTACCACAATGCTTCGGGCGTCTACCATGTCACCAATGACTGCCCAAATTCAAGCATAGTGTTTGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCGCGCTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCTCTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGTCTGCTCAGCCTTTTACATCGGGGATTTGTGTGGTGGCGTGTTCTTGGTCGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACTACCCAAGACTGCAATTGTTCCATCTATGCAGGGCACATTACG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271828i_0922"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTATCGCAATGTCTCGGGCATTTACCACATCACCAATGACTGCCCGAATTCAAGCATAGTGTTTGAGGCCGATCACCACATCTTACACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCGCGTTGCTGGGTGGCCCTAACTCCTACCGTCGCAGCGCCGTACATCGGCGCACCACTTGAGTCCTTACGGAGTCATGTGGATTTGATGGTGGGGGCTGCCACTGCTTGTTCGGCCCTTTACATCGGGGATTTGTGTGGTGGCTTGTTCCTGGTTGGTCAGATGTTCTCCTTCCGACCACGGCGCCACTGGACTACCCAGGAATGCAATTGCTCCATCTATTCAGGACACCTCACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271827i_0883"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCACCTCGGCCATTAACTATCGCAATGCTTCGGGCGTTTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCACGCTGCTGGGTGGCCCTTACCCCCACCGTCGCAGCGCCATACATCGGCGCGCCACTTCAATCTCTACGGAGTCATGTGGATTTGATGGTGGGGGCCGCCACTGCTTGTTCAGCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTCGGTCAGATGTTCTCTTTCCGGCCACGGCGCCACTGGACTACCCAGGACTGCAATTGTTCCATCTATACAGGGCACATCATG
+		</sequence>
+		<sequence>
+			<taxon idref="AF271826i_0873"/>
+			CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTACCACAATGTTTCGGGCATCTACCATGTCACCAATGACTGCCCAAATTCAAGCATAGTGTATGAGGCCGACCATCACATCCTACACCTCCCAGGTTGCGTGCCCTGCGTGAGGACGGGGAACCAGTCGCACTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGAGTCATGTGGATCTGATGGTAGGGGCTGCCACTGTTTGTTCAGCCCTTTATATCGGGGATTTGTGTGGCGGCTTGTTTTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACCACCCAGGATTGCAATTGTTCCATCTATACGGGGCACATTACT
+		</sequence>
+		<sequence>
+			<taxon idref="AF271825i_0800"/>
+			CTCTTGGCACTTCTTTCGTGCTTGACTGTCCCCGCTTCGGCCATCAACTACCGCAATGCTTCGGGCGTCTACCACGTCACCAACGACTGCCCGAATTCAAGCATAGTGTTTGAGGCCGACCATCACATCTTACACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCTCGTTGCTGGGTGGCTCTTACTCCTACTGTCGCAGCGCCACACATCGGCGCGCCGCTTGAATCCTTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGCTTGTTCGGCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTCGGTCAGATGTTCTCTTTCCGACCACGACGCCACTGGACTACCCAGGACTGCAATTGTTCTATCTATACAGGGCACATCACT
+		</sequence>
+	</alignment>
+	
+	
+
+	<!-- The unique patterns from 1 to end                                       -->
+	<!-- npatterns=246                                                           -->
+	<patterns id="patterns" from="1" strip="false">
+		<alignment idref="alignment"/>
+	</patterns>
+	
+
+	<!-- This is a simple constant population size coalescent model              -->
+	<!-- that is used to generate an initial tree for the chain.                 -->
+	<constantSize id="initialDemo" units="years">
+		<populationSize>
+			<parameter id="initialDemo.popSize" value="100.0"/>
+		</populationSize>
+	</constantSize>
+	
+
+	<!-- Construct a starting tree that is compatible with specified clade heights-->
+	<rescaledTree id="startingTree">
+
+		<!-- Construct a rough-and-ready UPGMA tree as an starting tree              -->
+		<upgmaTree>
+			<distanceMatrix correction="JC">
+				<patterns>
+
+					<!-- To generate UPGMA starting tree, only use the 1st aligment, which may be 1 of many aligments using this tree.-->
+					<alignment idref="alignment"/>
+				</patterns>
+			</distanceMatrix>
+		</upgmaTree>
+	</rescaledTree>
+	
+
+	<!-- Generate a tree model                                                   -->
+	<treeModel id="treeModel">
+		<upgmaTree idref="startingTree"/>
+		<rootHeight>
+			<parameter id="treeModel.rootHeight"/>
+		</rootHeight>
+		<nodeHeights internalNodes="true">
+			<parameter id="treeModel.internalNodeHeights"/>
+		</nodeHeights>
+		<nodeHeights internalNodes="true" rootNode="true">
+			<parameter id="treeModel.allInternalNodeHeights"/>
+		</nodeHeights>
+	</treeModel>
+
+	<!-- Statistic for sum of the branch lengths of the tree (tree length)       -->
+	<treeLengthStatistic id="treeLength">
+		<treeModel idref="treeModel"/>
+	</treeLengthStatistic>
+	
+	
+
+	<!-- Generate a variableDemographic for extended Bayesian skyline process    -->
+	<variableDemographic id="demographic" type="stepwise" useMidpoints="false">
+		<populationSizes>
+
+			<!-- popSize value = populationMean value                                    -->
+			<parameter id="demographic.popSize" value="1.0"/>
+		</populationSizes>
+		<indicators>
+			<parameter id="demographic.indicators" value="0.0"/>
+		</indicators>
+		<trees>
+            <!-- autosomal, ploidy=2, default by beauti -->
+			<ptree ploidy="1.0">
+				<treeModel idref="treeModel"/>
+			</ptree>
+		</trees>
+	</variableDemographic>
+	<coalescentLikelihood id="coalescent">
+		<model>
+			<variableDemographic idref="demographic"/>
+		</model>
+
+		<!-- Take population Tree from demographic                                   -->
+	</coalescentLikelihood>
+	<sumStatistic id="demographic.populationSizeChanges" elementwise="true">
+		<parameter idref="demographic.indicators"/>
+	</sumStatistic>
+	<exponentialDistributionModel id="demographic.populationMeanDist">
+		<mean>
+
+			<!-- prefer populationMean value = 1                                         -->
+			<parameter id="demographic.populationMean" value="1.0"/>
+		</mean>
+	</exponentialDistributionModel>
+
+	<!-- The strict clock (Uniform rates across branches)                        -->
+	<strictClockBranchRates id="branchRates">
+		<rate>
+			<parameter id="clock.rate" value="1.0"/>
+		</rate>
+	</strictClockBranchRates>
+	
+<!-- 
+	<rateStatistic id="meanRate" name="meanRate" mode="mean" internal="true" external="true">
+		<treeModel idref="treeModel"/>
+		<strictClockBranchRates idref="branchRates"/>
+	</rateStatistic>
+ -->
+	
+
+	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
+	<HKYModel id="hky">
+		<frequencies>
+			<frequencyModel dataType="nucleotide">
+				<frequencies>
+					<parameter id="frequencies" value="0.25 0.25 0.25 0.25"/>
+				</frequencies>
+			</frequencyModel>
+		</frequencies>
+		<kappa>
+			<parameter id="kappa" value="2.0" lower="0.0"/>
+		</kappa>
+	</HKYModel>
+
+	<!-- site model                                                              -->
+	<siteModel id="siteModel">
+		<substitutionModel>
+			<HKYModel idref="hky"/>
+		</substitutionModel>
+	</siteModel>
+
+	<!-- 
+<statistic id="mu" name="mu">
+		<siteModel idref="siteModel"/>
+	</statistic>
+ -->
+
+	<!-- Likelihood for tree given sequence data                                 -->
+<!-- 
+	<treeDataLikelihood id="treeLikelihood" useAmbiguities="false">
+		<partition>
+			<patterns idref="patterns"/>
+			<siteModel idref="siteModel"/>
+		</partition>
+		<treeModel idref="treeModel"/>
+		<strictClockBranchRates idref="branchRates"/>
+	</treeDataLikelihood>
+ -->
+	<treeLikelihood id="treeLikelihood" useAmbiguities="false">
+		<patterns idref="patterns"/>
+		<treeModel idref="treeModel"/>
+		<siteModel idref="siteModel"/>                 
+        <strictClockBranchRates idref="branchRates"/>
+	</treeLikelihood>	
+
+	<!-- Define operators                                                        -->
+	<operators id="operators" optimizationSchedule="default">
+		<scaleOperator scaleFactor="0.75" weight="1">
+			<parameter idref="kappa"/>
+		</scaleOperator>
+		<deltaExchange delta="0.01" weight="1">
+			<parameter idref="frequencies"/>
+		</deltaExchange>
+		<scaleOperator scaleFactor="0.75" scaleAll="true" ignoreBounds="true" weight="3">
+			<parameter idref="treeModel.allInternalNodeHeights"/>
+		</scaleOperator>
+		<subtreeSlide size="1.0" gaussian="true" weight="30">
+			<treeModel idref="treeModel"/>
+		</subtreeSlide>
+		<narrowExchange weight="30">
+			<treeModel idref="treeModel"/>
+		</narrowExchange>
+		<wideExchange weight="3">
+			<treeModel idref="treeModel"/>
+		</wideExchange>
+		<wilsonBalding weight="3">
+			<treeModel idref="treeModel"/>
+		</wilsonBalding>
+		<scaleOperator scaleFactor="0.75" weight="3">
+			<parameter idref="treeModel.rootHeight"/>
+		</scaleOperator>
+		<uniformOperator weight="30">
+			<parameter idref="treeModel.internalNodeHeights"/>
+		</uniformOperator>
+		<scaleOperator scaleFactor="0.9" weight="3">
+			<parameter idref="demographic.populationMean"/>
+		</scaleOperator>
+		<sampleNonActiveOperator weight="15">
+			<distribution>
+				<parameter idref="demographic.populationMeanDist"/>
+			</distribution>
+			<data>
+				<parameter idref="demographic.popSize"/>
+			</data>
+			<indicators>
+				<parameter idref="demographic.indicators"/>
+			</indicators>
+		</sampleNonActiveOperator>
+		<bitFlipOperator weight="60">
+			<parameter idref="demographic.indicators"/>
+		</bitFlipOperator>
+		<scaleOperator scaleFactor="0.5" weight="6">
+			<parameter idref="demographic.popSize"/>
+			<indicators pickoneprob="1.0">
+				<parameter idref="demographic.indicators"/>
+			</indicators>
+		</scaleOperator>
+	</operators>
+	
+
+	<!-- Define MCMC                                                             -->
+	<mcmc id="mcmc" chainLength="100000000" autoOptimize="true" operatorAnalysis="hcv.ops">
+		<posterior id="posterior">
+			<prior id="prior">
+				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
+					<parameter idref="kappa"/>
+				</logNormalPrior>
+				<uniformPrior lower="0.0" upper="1.0">
+					<parameter idref="frequencies"/>
+				</uniformPrior>
+				<poissonPrior mean="0.6931471805599453" offset="0.0">
+					<statistic idref="demographic.populationSizeChanges"/>
+				</poissonPrior>
+				<oneOnXPrior>
+					<parameter idref="demographic.populationMean"/>
+				</oneOnXPrior>
+				<coalescentLikelihood idref="coalescent"/>
+				
+				<mixedDistributionLikelihood>
+					<distribution0>
+						<exponentialDistributionModel idref="demographic.populationMeanDist"/>
+					</distribution0>
+					<distribution1>
+						<exponentialDistributionModel idref="demographic.populationMeanDist"/>
+					</distribution1>
+					<data>
+						<parameter idref="demographic.popSize"/>
+					</data>
+					<indicators>
+						<parameter idref="demographic.indicators"/>
+					</indicators>
+				</mixedDistributionLikelihood>
+				
+			</prior>
+			<likelihood id="likelihood">
+<!-- 				<treeDataLikelihood idref="treeLikelihood"/> -->
+                 <treeLikelihood idref="treeLikelihood"/>
+
+			</likelihood>
+		</posterior>
+		<operators idref="operators"/>
+
+		<!-- write log to screen                                                     -->
+		<log id="screenLog" logEvery="5000000">
+			<column label="posterior" dp="4" width="12">
+				<posterior idref="posterior"/>
+			</column>
+			<column label="Prior" dp="4" width="12">
+				<prior idref="prior"/>
+			</column>
+			<column label="Likelihood" dp="4" width="12">
+				<likelihood idref="likelihood"/>
+			</column>
+			<column label="rootHeight" sf="6" width="12">
+				<parameter idref="treeModel.rootHeight"/>
+			</column>
+		</log>
+
+		<!-- write log to file                                                       -->
+		<log id="fileLog" logEvery="25000" fileName="hcv.log" overwrite="false">
+			<posterior idref="posterior"/>
+			<likelihood idref="likelihood"/>
+			<prior idref="prior"/>
+			
+			<treeLikelihood idref="treeLikelihood"/>
+			<parameter idref="treeModel.rootHeight"/>
+			<treeLengthStatistic idref="treeLength"/>
+			
+			<coalescentLikelihood idref="coalescent"/>
+			<sumStatistic idref="demographic.populationSizeChanges"/>
+			<parameter idref="demographic.populationMean"/>
+			<parameter idref="demographic.popSize"/>
+			<parameter idref="demographic.indicators"/>
+			
+			<parameter idref="kappa"/>
+			<parameter idref="frequencies"/>
+						
+		</log>
+
+		<!-- write tree log to file                                                  -->
+		<logTree id="treeFileLog" logEvery="25000" nexusFormat="true" fileName="hcv.trees" sortTranslationTable="true">
+			<treeModel idref="treeModel"/>
+			<trait name="rate" tag="rate">
+				<strictClockBranchRates idref="branchRates"/>
+			</trait>
+			<posterior idref="posterior"/>
+		</logTree>
+
+	</mcmc>
+	
+	<report>
+		<property name="timer">
+			<mcmc idref="mcmc"/>
+		</property>
+	</report>
+	
+	<VDAnalysis id="demographic.analysis" burnIn="0.3" useMidpoints="false">
+		<logFileName>
+			hcv.log
+		</logFileName>
+		<treeFileNames>
+			<treeOfLoci>
+				hcv.trees
+			</treeOfLoci>
+		</treeFileNames>
+		<populationModelType>
+			stepwise
+		</populationModelType>
+		<populationFirstColumn>
+			demographic.popSize1
+		</populationFirstColumn>
+		<indicatorsFirstColumn>
+			demographic.indicators1
+		</indicatorsFirstColumn>
+	</VDAnalysis>
+	<CSVexport fileName="hcv.csv" separator=",">
+		<columns>
+			<VDAnalysis idref="demographic.analysis"/>
+		</columns>
+	</CSVexport>
+
+</beast>
diff -Nru beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/beast1/testEBSP-old.xml beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/beast1/testEBSP-old.xml
--- beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/beast1/testEBSP-old.xml	1970-01-01 00:00:00.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/beast1/testEBSP-old.xml	2022-04-04 07:18:36.000000000 +0000
@@ -0,0 +1,836 @@
+<?xml version="1.0" standalone="yes"?>
+
+<!-- Generated by BEAUTi v1.7.0 Prerelease r3910                             -->
+<!--       by Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard         -->
+<!--       Department of Computer Science, University of Auckland and        -->
+<!--       Institute of Evolutionary Biology, University of Edinburgh        -->
+<!--       David Geffen School of Medicine, University of California, Los Angeles-->
+<!--       http://beast.bio.ed.ac.uk/                                        -->
+<beast>
+
+	<!-- The list of taxa to be analysed (can also include dates/ages).          -->
+	<!-- ntax=26                                                                 -->
+	<taxa id="taxa">
+		<taxon id="Orthogeomys_heterodus"/>
+		<taxon id="Thomomys_bottae_awahnee_a"/>
+		<taxon id="Thomomys_bottae_awahnee_b"/>
+		<taxon id="Thomomys_bottae_xerophilus"/>
+		<taxon id="Thomomys_bottae_cactophilus"/>
+		<taxon id="Thomomys_bottae_albatus"/>
+		<taxon id="Thomomys_bottae_ruidosae"/>
+		<taxon id="Thomomys_bottae_bottae"/>
+		<taxon id="Thomomys_bottae_alpinus"/>
+		<taxon id="Thomomys_bottae_riparius"/>
+		<taxon id="Thomomys_bottae_mewa"/>
+		<taxon id="Thomomys_bottae_saxatilis"/>
+		<taxon id="Thomomys_bottae_laticeps"/>
+		<taxon id="Thomomys_talpoides_ocius"/>
+		<taxon id="Thomomys_idahoensis_pygmaeus_a"/>
+		<taxon id="Thomomys_idahoensis_pygmaeus_b"/>
+		<taxon id="Thomomys_mazama_mazama"/>
+		<taxon id="Thomomys_mazama_nasicus"/>
+		<taxon id="Thomomys_monticola_a"/>
+		<taxon id="Thomomys_monticola_b"/>
+		<taxon id="Thomomys_talpoides_yakimensis"/>
+		<taxon id="Thomomys_talpoides_bridgeri"/>
+		<taxon id="Thomomys_townsendii_townsendii"/>
+		<taxon id="Thomomys_townsendii_relictus"/>
+		<taxon id="Thomomys_umbrinus_chihuahuae"/>
+		<taxon id="Thomomys_umbrinus_atroavarius"/>
+	</taxa>
+
+	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
+	<!-- ntax=26 nchar=614                                                       -->
+	<alignment id="alignment1" dataType="nucleotide">
+		<sequence>
+			<taxon idref="Orthogeomys_heterodus"/>
+			ATTCTAGGCAAAAAG-AGCAATGCTGGAGGTATTACAATACCAGACTTCAAACTTTACTATAGAGCCATAATAACAAAAACCGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAATGGAAYAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGTCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCACCATGCACAGGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCAGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGGGAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATAGGAGAAAGACTCAATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAATAATACATCTGACAAATGCTTGAT--ATCCAGT-ATCTACAGGGAACTCAAGAAATTAATC
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_awahnee_a"/>
+			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACMCAGTCTATTCAATTATTGGKGCTGGCAAAACTGGGCAGCCMCATGCARAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_awahnee_b"/>
+			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCM-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGT????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_xerophilus"/>
+			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAAYTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_cactophilus"/>
+			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAAYTGTTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAA????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_albatus"/>
+			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGATCCAGAAATAGAACCAC-ATACCTATAGTCAACTTGTATTTGATAAAGGAGCTAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCATTTCACCATGCACAAGAATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCT-------------------------------------CATAGGCACTCATAGGCACAGGCAAAAGATTCCTATACAGGAACCCAGGGTCAACAACAGATTGGAGAGAGACTCAATAAATGGGACTACCTAAAAATAAAA-GTTTCTGCAC?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_ruidosae"/>
+			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCARAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAAYTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAG??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_bottae"/>
+			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAAATTCCTGAACAGAATCCCAGGGTCA-CAACAGATKGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATA?????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_alpinus"/>
+			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCTATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCA??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_riparius"/>
+			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACA???????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_mewa"/>
+			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCATTTCACCATGCACAAGAATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAA???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_saxatilis"/>
+			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_laticeps"/>
+			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAATTGCTACATGATAAWGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCAATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATAT????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_talpoides_ocius"/>
+			???CTAGGCAAAA-G-AGC-ATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CKCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
+			????????CAAAA-G-AGCAATGCTGGTGGTATYACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
+			????GGCGCAAAA-G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGCTATCTACAGAGAACTCAAGAAACTAATC
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_mazama_mazama"/>
+			ATTCTAGGCAAAAAGAAGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_mazama_nasicus"/>
+			ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCSCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTA-TC
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_monticola_a"/>
+			??????????????G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGYCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_monticola_b"/>
+			ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATYACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAWATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAATGGAACRAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATATATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_talpoides_yakimensis"/>
+			ATTCTAGGCAAAA-G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTKTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_talpoides_bridgeri"/>
+			ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATCCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_townsendii_townsendii"/>
+			ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTYGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTCTGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCCACAATACATCTGACAAATGCTTAAT--ATCCAGT-ATCTACAGG-AACTCAAG?????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_townsendii_relictus"/>
+			??????????????G-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTAYTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCACTATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAATGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAATTGCTACATGATAAWGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAATGTTTCTGTACAGATAAAAACATAG???????????????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_umbrinus_chihuahuae"/>
+			?????????????AG-AGC-ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCTTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATACATCTGACAAATGCTTAAT--ATCCAGT-ATCTACA????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_umbrinus_atroavarius"/>
+			ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGCATTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGKCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGYCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAATTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCCACAATACATCTGACAAATGCTT-ATATATCCAGT-ATCTACAGAGAACTCAAG?????????
+		</sequence>
+	</alignment>
+
+	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
+	<!-- ntax=26 nchar=601                                                       -->
+	<alignment id="alignment2" dataType="nucleotide">
+		<sequence>
+			<taxon idref="Orthogeomys_heterodus"/>
+			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCACAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCGTTTCTGGAAAACTGAGATCTTGTTTTGACCAACAGAAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGATGTCTCTGTCAGGATCTAGTCCCATCCTG-AATCCATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTCAGAACTGACTGAATCAGGCCAGTGAAAGTTA-CAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATTGTGCATGGCTTCATTAGCAGGTTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCATCAGATTGTCAGGGTCTTGGATTCTGATAAGTTCTGTGTTCCTGATGAGAGACTGGTTATTCAGTAAGTTGTAGGACAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_awahnee_a"/>
+			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGAGAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_awahnee_b"/>
+			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGAKAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_xerophilus"/>
+			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCACTAAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTRTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_cactophilus"/>
+			C-AGCTTGCTG-TCACACTACCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCACTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCASTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_albatus"/>
+			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGTGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_ruidosae"/>
+			?????????????????????????????C-AGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_bottae"/>
+			C-AGCTTGCTG-TCACACYGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTAKGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCRTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_alpinus"/>
+			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCC-AGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGTTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCYACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_riparius"/>
+			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_mewa"/>
+			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAATTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_saxatilis"/>
+			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_laticeps"/>
+			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_talpoides_ocius"/>
+			C-AGCTTGCTGGTCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCATATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAAWGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGACAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
+			C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTTTAAGTGTTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGTCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGTCCAGTGAAACTTAACAGCTACCTTGCCAATKGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGG--TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCGGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
+			CAAGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTGTTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGTCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGG--TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCGGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_mazama_mazama"/>
+			C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTATTGCCTGGATATAGTGTCTATAGACAGAGACAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCACATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCACCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAG-CGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_mazama_nasicus"/>
+			C-AGCTTGCTG-TCACAATGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTATTGCCTGGATATAGTGTCTATAGACAGAGACAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCACATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAG-CGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_monticola_a"/>
+			C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGACGCCKTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAGGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_monticola_b"/>
+			C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGACGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTYCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAGGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_talpoides_yakimensis"/>
+			C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGAMTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_talpoides_bridgeri"/>
+			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_townsendii_townsendii"/>
+			C-AGCTTGCTGGTCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_townsendii_relictus"/>
+			C-AGCTTGCTGGTCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_umbrinus_chihuahuae"/>
+			C-AGCTTGCTGGTCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAAGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTGGAATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGAGGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_umbrinus_atroavarius"/>
+			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
+		</sequence>
+	</alignment>
+
+	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
+	<!-- ntax=26 nchar=819                                                       -->
+	<alignment id="alignment3" dataType="nucleotide">
+		<sequence>
+			<taxon idref="Orthogeomys_heterodus"/>
+			CATGATTTTGTCATGCCTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGATGATTGACGCTGCTGTCAGTAGTGAGTGACACAAATTTTATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACGTGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAATTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATTTCTTTTCCA-CC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGATTTTATGGGACTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTAYCTGAAGGTTATTGATGGTGACCTCATTTTCTTGTGCTTGTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAATTCAGAGTTTGAACACTGTCCTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTCTATGTATGTGGTACCGTGCACTCAAACCCAGGTCTTTGTGAATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGCAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_awahnee_a"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACARAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGACGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_awahnee_b"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAMGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_xerophilus"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_cactophilus"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_albatus"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_ruidosae"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTYGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_bottae"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTYGTTTTCACCTGTGTGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCYGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGGTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAYGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_alpinus"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCYGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAYGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_riparius"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_mewa"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_saxatilis"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTARGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_bottae_laticeps"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_talpoides_ocius"/>
+			CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTATTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTT--------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTC-TATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATCTCTTTGTCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTGTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGTA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
+			???????TTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTCGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------T--GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGACTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTA--------CCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTA?????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
+			?ATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACTAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTATACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATGTTTTTTTT-G------------------------------CACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCACCACTTCTGGCTTTTTTTTTTCTACGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGCTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATTATGTTTGTGCAA????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_mazama_mazama"/>
+			??????????????????????A---GCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------------------------------------------------------------------------------TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAAGCACTTTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGTTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTT?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_mazama_nasicus"/>
+			??????????????GCTTTCTTACGTGCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCTTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAGGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTGTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTCC---------GGTACCATGCACTGGAACCCAGGTCTTCGTGCATGCTGGACAGCAACTCTACCACTAGGCAAAGCTTCTGGACCCATTAGT?????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_monticola_a"/>
+			CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGATCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_monticola_b"/>
+			CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAAYGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTT--GCCAGTCCTGGGCTTSAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTKTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGAYCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCYAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_talpoides_yakimensis"/>
+			?????????????????TTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGCTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAGTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------TTTGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCAGTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGTCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAATACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCAC???????????????????????????????????????????????????????
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_talpoides_bridgeri"/>
+			CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTCGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCYCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_townsendii_townsendii"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACACAAATTTCATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCCTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTT--ATATCATCTTTGTGCAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_townsendii_relictus"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_umbrinus_chihuahuae"/>
+			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTRCCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
+		</sequence>
+		<sequence>
+			<taxon idref="Thomomys_umbrinus_atroavarius"/>
+			CATGATTTTGTCATGYTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTYGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTTYATATCATCTTTGTGAAACT-A
+		</sequence>
+	</alignment>
+
+	<!-- The unique patterns from 1 to end                                       -->
+	<!-- npatterns=144                                                           -->
+	<patterns id="26.patterns" from="1">
+		<alignment idref="alignment1"/>
+	</patterns>
+
+	<!-- The unique patterns from 1 to end                                       -->
+	<!-- npatterns=71                                                            -->
+	<patterns id="29.patterns" from="1">
+		<alignment idref="alignment2"/>
+	</patterns>
+
+	<!-- The unique patterns from 1 to end                                       -->
+	<!-- npatterns=153                                                           -->
+	<patterns id="47.patterns" from="1">
+		<alignment idref="alignment3"/>
+	</patterns>
+
+	<!-- This is a simple constant population size coalescent model              -->
+	<!-- that is used to generate an initial tree for the chain.                 -->
+	<constantSize id="initialDemo" units="substitutions">
+		<populationSize>
+			<parameter id="initialDemo.popSize" value="100.0"/>
+		</populationSize>
+	</constantSize>
+
+	<!-- Generate a random starting tree under the coalescent process            -->
+	<coalescentTree id="26.startingTree" rootHeight="0.017">
+		<taxa idref="taxa"/>
+		<constantSize idref="initialDemo"/>
+	</coalescentTree>
+
+	<!-- Generate a random starting tree under the coalescent process            -->
+	<coalescentTree id="29.startingTree" rootHeight="0.016">
+		<taxa idref="taxa"/>
+		<constantSize idref="initialDemo"/>
+	</coalescentTree>
+
+	<!-- Generate a random starting tree under the coalescent process            -->
+	<coalescentTree id="47.startingTree" rootHeight="0.017">
+		<taxa idref="taxa"/>
+		<constantSize idref="initialDemo"/>
+	</coalescentTree>
+
+	<!-- Generate a tree model                                                   -->
+	<treeModel id="26.treeModel">
+		<coalescentTree idref="26.startingTree"/>
+		<rootHeight>
+			<parameter id="26.treeModel.rootHeight"/>
+		</rootHeight>
+		<nodeHeights internalNodes="true">
+			<parameter id="26.treeModel.internalNodeHeights"/>
+		</nodeHeights>
+		<nodeHeights internalNodes="true" rootNode="true">
+			<parameter id="26.treeModel.allInternalNodeHeights"/>
+		</nodeHeights>
+	</treeModel>
+
+	<!-- Generate a tree model                                                   -->
+	<treeModel id="29.treeModel">
+		<coalescentTree idref="29.startingTree"/>
+		<rootHeight>
+			<parameter id="29.treeModel.rootHeight"/>
+		</rootHeight>
+		<nodeHeights internalNodes="true">
+			<parameter id="29.treeModel.internalNodeHeights"/>
+		</nodeHeights>
+		<nodeHeights internalNodes="true" rootNode="true">
+			<parameter id="29.treeModel.allInternalNodeHeights"/>
+		</nodeHeights>
+	</treeModel>
+
+	<!-- Generate a tree model                                                   -->
+	<treeModel id="47.treeModel">
+		<coalescentTree idref="47.startingTree"/>
+		<rootHeight>
+			<parameter id="47.treeModel.rootHeight"/>
+		</rootHeight>
+		<nodeHeights internalNodes="true">
+			<parameter id="47.treeModel.internalNodeHeights"/>
+		</nodeHeights>
+		<nodeHeights internalNodes="true" rootNode="true">
+			<parameter id="47.treeModel.allInternalNodeHeights"/>
+		</nodeHeights>
+	</treeModel>
+
+	<!-- Generate a variableDemographic for extended Bayesian skyline process    -->
+	<variableDemographic id="demographic" type="linear" useMidpoints="true">
+		<populationSizes>
+
+			<!-- popSize value = populationMean value                                    -->
+			<parameter id="demographic.popSize" value="0.017"/>
+		</populationSizes>
+		<indicators>
+			<parameter id="demographic.indicators" value="0.0"/>
+		</indicators>
+		<trees>
+			<ptree ploidy="2.0">
+				<treeModel idref="26.treeModel"/>
+			</ptree>
+			<ptree ploidy="2.0">
+				<treeModel idref="29.treeModel"/>
+			</ptree>
+			<ptree ploidy="2.0">
+				<treeModel idref="47.treeModel"/>
+			</ptree>
+		</trees>
+	</variableDemographic>
+	<coalescentLikelihood id="coalescent">
+		<model>
+			<variableDemographic idref="demographic"/>
+		</model>
+
+		<!-- Take population Tree from demographic                                   -->
+	</coalescentLikelihood>
+	<sumStatistic id="demographic.populationSizeChanges" elementwise="true">
+		<parameter idref="demographic.indicators"/>
+	</sumStatistic>
+	<exponentialDistributionModel id="demographic.populationMeanDist">
+		<mean>
+
+			<!-- prefer populationMean value = 1                                         -->
+			<parameter id="demographic.populationMean" value="0.017"/>
+		</mean>
+	</exponentialDistributionModel>
+
+	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
+	<HKYModel id="26.hky">
+		<frequencies>
+			<frequencyModel dataType="nucleotide">
+				<frequencies>
+					<parameter id="26.frequencies" value="0.25 0.25 0.25 0.25"/>
+				</frequencies>
+			</frequencyModel>
+		</frequencies>
+		<kappa>
+			<parameter id="26.kappa" value="2.0" lower="0.0"/>
+		</kappa>
+	</HKYModel>
+
+	<!-- site model                                                              -->
+	<siteModel id="26.siteModel">
+		<substitutionModel>
+			<HKYModel idref="26.hky"/>
+		</substitutionModel>
+	</siteModel>
+
+	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
+	<HKYModel id="29.hky">
+		<frequencies>
+			<frequencyModel dataType="nucleotide">
+				<frequencies>
+					<parameter id="29.frequencies" value="0.25 0.25 0.25 0.25"/>
+				</frequencies>
+			</frequencyModel>
+		</frequencies>
+		<kappa>
+			<parameter id="29.kappa" value="2.0" lower="0.0"/>
+		</kappa>
+	</HKYModel>
+
+	<!-- site model                                                              -->
+	<siteModel id="29.siteModel">
+		<substitutionModel>
+			<HKYModel idref="29.hky"/>
+		</substitutionModel>
+	</siteModel>
+
+	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
+	<HKYModel id="47.hky">
+		<frequencies>
+			<frequencyModel dataType="nucleotide">
+				<frequencies>
+					<parameter id="47.frequencies" value="0.25 0.25 0.25 0.25"/>
+				</frequencies>
+			</frequencyModel>
+		</frequencies>
+		<kappa>
+			<parameter id="47.kappa" value="2.0" lower="0.0"/>
+		</kappa>
+	</HKYModel>
+
+	<!-- site model                                                              -->
+	<siteModel id="47.siteModel">
+		<substitutionModel>
+			<HKYModel idref="47.hky"/>
+		</substitutionModel>
+	</siteModel>
+
+	<!-- Likelihood for tree given sequence data                                 -->
+	<treeLikelihood id="26.treeLikelihood" useAmbiguities="false">
+		<patterns idref="26.patterns"/>
+		<treeModel idref="26.treeModel"/>
+		<siteModel idref="26.siteModel"/>
+	</treeLikelihood>
+
+	<!-- Likelihood for tree given sequence data                                 -->
+	<treeLikelihood id="29.treeLikelihood" useAmbiguities="false">
+		<patterns idref="29.patterns"/>
+		<treeModel idref="29.treeModel"/>
+		<siteModel idref="29.siteModel"/>
+	</treeLikelihood>
+
+	<!-- Likelihood for tree given sequence data                                 -->
+	<treeLikelihood id="47.treeLikelihood" useAmbiguities="false">
+		<patterns idref="47.patterns"/>
+		<treeModel idref="47.treeModel"/>
+		<siteModel idref="47.siteModel"/>
+	</treeLikelihood>
+
+	<!-- Define operators                                                        -->
+	<operators id="operators">
+		<scaleOperator scaleFactor="0.75" weight="0.1">
+			<parameter idref="26.kappa"/>
+		</scaleOperator>
+		<deltaExchange delta="0.01" weight="0.1">
+			<parameter idref="26.frequencies"/>
+		</deltaExchange>
+		<scaleOperator scaleFactor="0.75" weight="0.1">
+			<parameter idref="29.kappa"/>
+		</scaleOperator>
+		<deltaExchange delta="0.01" weight="0.1">
+			<parameter idref="29.frequencies"/>
+		</deltaExchange>
+		<scaleOperator scaleFactor="0.75" weight="0.1">
+			<parameter idref="47.kappa"/>
+		</scaleOperator>
+		<deltaExchange delta="0.01" weight="0.1">
+			<parameter idref="47.frequencies"/>
+		</deltaExchange>
+		<upDownOperator scaleFactor="0.75" weight="30">
+			<up>
+			</up>
+			<down>
+				<parameter idref="demographic.populationMean"/>
+				<parameter idref="demographic.popSize"/>
+				<parameter idref="26.treeModel.allInternalNodeHeights"/>
+				<parameter idref="29.treeModel.allInternalNodeHeights"/>
+				<parameter idref="47.treeModel.allInternalNodeHeights"/>
+			</down>
+		</upDownOperator>
+		<subtreeSlide size="0.0017" gaussian="true" weight="15">
+			<treeModel idref="26.treeModel"/>
+		</subtreeSlide>
+		<narrowExchange weight="15">
+			<treeModel idref="26.treeModel"/>
+		</narrowExchange>
+		<wideExchange weight="3">
+			<treeModel idref="26.treeModel"/>
+		</wideExchange>
+		<wilsonBalding weight="3">
+			<treeModel idref="26.treeModel"/>
+		</wilsonBalding>
+		<scaleOperator scaleFactor="0.75" weight="3">
+			<parameter idref="26.treeModel.rootHeight"/>
+		</scaleOperator>
+		<uniformOperator weight="30">
+			<parameter idref="26.treeModel.internalNodeHeights"/>
+		</uniformOperator>
+		<subtreeSlide size="0.0016" gaussian="true" weight="15">
+			<treeModel idref="29.treeModel"/>
+		</subtreeSlide>
+		<narrowExchange weight="15">
+			<treeModel idref="29.treeModel"/>
+		</narrowExchange>
+		<wideExchange weight="3">
+			<treeModel idref="29.treeModel"/>
+		</wideExchange>
+		<wilsonBalding weight="3">
+			<treeModel idref="29.treeModel"/>
+		</wilsonBalding>
+		<scaleOperator scaleFactor="0.75" weight="3">
+			<parameter idref="29.treeModel.rootHeight"/>
+		</scaleOperator>
+		<uniformOperator weight="30">
+			<parameter idref="29.treeModel.internalNodeHeights"/>
+		</uniformOperator>
+		<subtreeSlide size="0.0017" gaussian="true" weight="15">
+			<treeModel idref="47.treeModel"/>
+		</subtreeSlide>
+		<narrowExchange weight="15">
+			<treeModel idref="47.treeModel"/>
+		</narrowExchange>
+		<wideExchange weight="3">
+			<treeModel idref="47.treeModel"/>
+		</wideExchange>
+		<wilsonBalding weight="3">
+			<treeModel idref="47.treeModel"/>
+		</wilsonBalding>
+		<scaleOperator scaleFactor="0.75" weight="3">
+			<parameter idref="47.treeModel.rootHeight"/>
+		</scaleOperator>
+		<uniformOperator weight="30">
+			<parameter idref="47.treeModel.internalNodeHeights"/>
+		</uniformOperator>
+		<scaleOperator scaleFactor="0.9" weight="3">
+			<parameter idref="demographic.populationMean"/>
+		</scaleOperator>
+		<sampleNonActiveOperator weight="15">
+			<distribution>
+				<parameter idref="demographic.populationMeanDist"/>
+			</distribution>
+			<data>
+				<parameter idref="demographic.popSize"/>
+			</data>
+			<indicators>
+				<parameter idref="demographic.indicators"/>
+			</indicators>
+		</sampleNonActiveOperator>
+		<bitFlipOperator weight="30">
+			<parameter idref="demographic.indicators"/>
+		</bitFlipOperator>
+		<scaleOperator scaleFactor="0.5" weight="6">
+			<parameter idref="demographic.popSize"/>
+			<indicators pickoneprob="1.0">
+				<parameter idref="demographic.indicators"/>
+			</indicators>
+		</scaleOperator>
+	</operators>
+
+	<!-- Define MCMC                                                             -->
+	<mcmc id="mcmc" chainLength="10000000" autoOptimize="true">
+		<posterior id="posterior">
+			<prior id="prior">
+				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
+					<parameter idref="26.kappa"/>
+				</logNormalPrior>
+				<uniformPrior lower="0.0" upper="1.0">
+					<parameter idref="26.frequencies"/>
+				</uniformPrior>
+				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
+					<parameter idref="29.kappa"/>
+				</logNormalPrior>
+				<uniformPrior lower="0.0" upper="1.0">
+					<parameter idref="29.frequencies"/>
+				</uniformPrior>
+				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
+					<parameter idref="47.kappa"/>
+				</logNormalPrior>
+				<uniformPrior lower="0.0" upper="1.0">
+					<parameter idref="47.frequencies"/>
+				</uniformPrior>
+				<poissonPrior mean="0.6931471805599453" offset="0.0">
+					<statistic idref="demographic.populationSizeChanges"/>
+				</poissonPrior>
+				<oneOnXPrior>
+					<parameter idref="demographic.populationMean"/>
+				</oneOnXPrior>
+				<coalescentLikelihood idref="coalescent"/>
+				<mixedDistributionLikelihood>
+					<distribution0>
+						<exponentialDistributionModel idref="demographic.populationMeanDist"/>
+					</distribution0>
+					<distribution1>
+						<exponentialDistributionModel idref="demographic.populationMeanDist"/>
+					</distribution1>
+					<data>
+						<parameter idref="demographic.popSize"/>
+					</data>
+					<indicators>
+						<parameter idref="demographic.indicators"/>
+					</indicators>
+				</mixedDistributionLikelihood>
+			</prior>
+			<likelihood id="likelihood">
+				<treeLikelihood idref="26.treeLikelihood"/>
+				<treeLikelihood idref="29.treeLikelihood"/>
+				<treeLikelihood idref="47.treeLikelihood"/>
+			</likelihood>
+		</posterior>
+		<operators idref="operators"/>
+
+		<!-- write log to screen                                                     -->
+		<log id="screenLog" logEvery="100000">
+			<column label="Posterior" dp="4" width="12">
+				<posterior idref="posterior"/>
+			</column>
+			<column label="Prior" dp="4" width="12">
+				<prior idref="prior"/>
+			</column>
+			<column label="Likelihood" dp="4" width="12">
+				<likelihood idref="likelihood"/>
+			</column>
+			<column label="26.rootHeight" sf="6" width="12">
+				<parameter idref="26.treeModel.rootHeight"/>
+			</column>
+			<column label="29.rootHeight" sf="6" width="12">
+				<parameter idref="29.treeModel.rootHeight"/>
+			</column>
+			<column label="47.rootHeight" sf="6" width="12">
+				<parameter idref="47.treeModel.rootHeight"/>
+			</column>
+		</log>
+
+		<!-- write log to file                                                       -->
+		<log id="fileLog" logEvery="1000" fileName="testEBSP.log" overwrite="false">
+			<posterior idref="posterior"/>
+			<prior idref="prior"/>
+			<likelihood idref="likelihood"/>
+			<parameter idref="26.treeModel.rootHeight"/>
+			<parameter idref="29.treeModel.rootHeight"/>
+			<parameter idref="47.treeModel.rootHeight"/>
+			<sumStatistic idref="demographic.populationSizeChanges"/>
+			<parameter idref="demographic.populationMean"/>
+			<parameter idref="demographic.popSize"/>
+			<parameter idref="demographic.indicators"/>
+			<parameter idref="26.kappa"/>
+			<parameter idref="26.frequencies"/>
+			<parameter idref="29.kappa"/>
+			<parameter idref="29.frequencies"/>
+			<parameter idref="47.kappa"/>
+			<parameter idref="47.frequencies"/>
+			<treeLikelihood idref="26.treeLikelihood"/>
+			<treeLikelihood idref="29.treeLikelihood"/>
+			<treeLikelihood idref="47.treeLikelihood"/>
+			<coalescentLikelihood idref="coalescent"/>
+		</log>
+
+		<!-- write tree log to file
+		<logTree id="26.treeFileLog" logEvery="1000" nexusFormat="true" fileName="testEBSP.26.trees" sortTranslationTable="true">
+			<treeModel idref="26.treeModel"/>
+			<posterior idref="posterior"/>
+		</logTree>
+		<logTree id="29.treeFileLog" logEvery="1000" nexusFormat="true" fileName="testEBSP.29.trees" sortTranslationTable="true">
+			<treeModel idref="29.treeModel"/>
+			<posterior idref="posterior"/>
+		</logTree>
+		<logTree id="47.treeFileLog" logEvery="1000" nexusFormat="true" fileName="testEBSP.47.trees" sortTranslationTable="true">
+			<treeModel idref="47.treeModel"/>
+			<posterior idref="posterior"/>
+		</logTree>  -->
+	</mcmc>
+	<report>
+		<property name="timer">
+			<mcmc idref="mcmc"/>
+		</property>
+	</report>
+<!-- 	<VDAnalysis id="demographic.analysis" burnIn="0.1" useMidpoints="true">
+		<logFileName>
+			testEBSP.log
+		</logFileName>
+		<treeFileNames>
+			<treeOfLoci>
+				testEBSP.26.trees
+			</treeOfLoci>
+			<treeOfLoci>
+				testEBSP.29.trees
+			</treeOfLoci>
+			<treeOfLoci>
+				testEBSP.47.trees
+			</treeOfLoci>
+		</treeFileNames>
+		<populationModelType>
+			linear
+		</populationModelType>
+		<populationFirstColumn>
+			demographic.popSize1
+		</populationFirstColumn>
+		<indicatorsFirstColumn>
+			demographic.indicators1
+		</indicatorsFirstColumn>
+	</VDAnalysis>
+	<CSVexport fileName="testEBSP.csv" separator=",">
+		<columns>
+			<VDAnalysis idref="demographic.analysis"/>
+		</columns>
+	</CSVexport> -->
+</beast>
diff -Nru beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/beast1/testEBSP.xml beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/beast1/testEBSP.xml
--- beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/beast1/testEBSP.xml	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/beast1/testEBSP.xml	1970-01-01 00:00:00.000000000 +0000
@@ -1,836 +0,0 @@
-<?xml version="1.0" standalone="yes"?>
-
-<!-- Generated by BEAUTi v1.7.0 Prerelease r3910                             -->
-<!--       by Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard         -->
-<!--       Department of Computer Science, University of Auckland and        -->
-<!--       Institute of Evolutionary Biology, University of Edinburgh        -->
-<!--       David Geffen School of Medicine, University of California, Los Angeles-->
-<!--       http://beast.bio.ed.ac.uk/                                        -->
-<beast>
-
-	<!-- The list of taxa to be analysed (can also include dates/ages).          -->
-	<!-- ntax=26                                                                 -->
-	<taxa id="taxa">
-		<taxon id="Orthogeomys_heterodus"/>
-		<taxon id="Thomomys_bottae_awahnee_a"/>
-		<taxon id="Thomomys_bottae_awahnee_b"/>
-		<taxon id="Thomomys_bottae_xerophilus"/>
-		<taxon id="Thomomys_bottae_cactophilus"/>
-		<taxon id="Thomomys_bottae_albatus"/>
-		<taxon id="Thomomys_bottae_ruidosae"/>
-		<taxon id="Thomomys_bottae_bottae"/>
-		<taxon id="Thomomys_bottae_alpinus"/>
-		<taxon id="Thomomys_bottae_riparius"/>
-		<taxon id="Thomomys_bottae_mewa"/>
-		<taxon id="Thomomys_bottae_saxatilis"/>
-		<taxon id="Thomomys_bottae_laticeps"/>
-		<taxon id="Thomomys_talpoides_ocius"/>
-		<taxon id="Thomomys_idahoensis_pygmaeus_a"/>
-		<taxon id="Thomomys_idahoensis_pygmaeus_b"/>
-		<taxon id="Thomomys_mazama_mazama"/>
-		<taxon id="Thomomys_mazama_nasicus"/>
-		<taxon id="Thomomys_monticola_a"/>
-		<taxon id="Thomomys_monticola_b"/>
-		<taxon id="Thomomys_talpoides_yakimensis"/>
-		<taxon id="Thomomys_talpoides_bridgeri"/>
-		<taxon id="Thomomys_townsendii_townsendii"/>
-		<taxon id="Thomomys_townsendii_relictus"/>
-		<taxon id="Thomomys_umbrinus_chihuahuae"/>
-		<taxon id="Thomomys_umbrinus_atroavarius"/>
-	</taxa>
-
-	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
-	<!-- ntax=26 nchar=614                                                       -->
-	<alignment id="alignment1" dataType="nucleotide">
-		<sequence>
-			<taxon idref="Orthogeomys_heterodus"/>
-			ATTCTAGGCAAAAAG-AGCAATGCTGGAGGTATTACAATACCAGACTTCAAACTTTACTATAGAGCCATAATAACAAAAACCGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAATGGAAYAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGTCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCACCATGCACAGGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCAGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGGGAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATAGGAGAAAGACTCAATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAATAATACATCTGACAAATGCTTGAT--ATCCAGT-ATCTACAGGGAACTCAAGAAATTAATC
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_awahnee_a"/>
-			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACMCAGTCTATTCAATTATTGGKGCTGGCAAAACTGGGCAGCCMCATGCARAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_awahnee_b"/>
-			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCM-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGT????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_xerophilus"/>
-			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAAYTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_cactophilus"/>
-			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAAYTGTTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAA????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_albatus"/>
-			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGATCCAGAAATAGAACCAC-ATACCTATAGTCAACTTGTATTTGATAAAGGAGCTAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCATTTCACCATGCACAAGAATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCT-------------------------------------CATAGGCACTCATAGGCACAGGCAAAAGATTCCTATACAGGAACCCAGGGTCAACAACAGATTGGAGAGAGACTCAATAAATGGGACTACCTAAAAATAAAA-GTTTCTGCAC?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_ruidosae"/>
-			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCARAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAAYTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAG??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_bottae"/>
-			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAAATTCCTGAACAGAATCCCAGGGTCA-CAACAGATKGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATA?????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_alpinus"/>
-			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCTATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCA??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_riparius"/>
-			????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACA???????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_mewa"/>
-			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCATTTCACCATGCACAAGAATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAA???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_saxatilis"/>
-			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_laticeps"/>
-			????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAATTGCTACATGATAAWGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCAATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATAT????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_talpoides_ocius"/>
-			???CTAGGCAAAA-G-AGC-ATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CKCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
-			????????CAAAA-G-AGCAATGCTGGTGGTATYACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
-			????GGCGCAAAA-G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGCTATCTACAGAGAACTCAAGAAACTAATC
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_mazama_mazama"/>
-			ATTCTAGGCAAAAAGAAGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_mazama_nasicus"/>
-			ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCSCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTA-TC
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_monticola_a"/>
-			??????????????G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGYCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_monticola_b"/>
-			ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATYACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAWATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAATGGAACRAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATATATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_talpoides_yakimensis"/>
-			ATTCTAGGCAAAA-G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTKTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_talpoides_bridgeri"/>
-			ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATCCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_townsendii_townsendii"/>
-			ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTYGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTCTGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCCACAATACATCTGACAAATGCTTAAT--ATCCAGT-ATCTACAGG-AACTCAAG?????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_townsendii_relictus"/>
-			??????????????G-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTAYTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCACTATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAATGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAATTGCTACATGATAAWGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAATGTTTCTGTACAGATAAAAACATAG???????????????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_umbrinus_chihuahuae"/>
-			?????????????AG-AGC-ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCTTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATACATCTGACAAATGCTTAAT--ATCCAGT-ATCTACA????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_umbrinus_atroavarius"/>
-			ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGCATTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGKCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGYCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAATTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCCACAATACATCTGACAAATGCTT-ATATATCCAGT-ATCTACAGAGAACTCAAG?????????
-		</sequence>
-	</alignment>
-
-	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
-	<!-- ntax=26 nchar=601                                                       -->
-	<alignment id="alignment2" dataType="nucleotide">
-		<sequence>
-			<taxon idref="Orthogeomys_heterodus"/>
-			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCACAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCGTTTCTGGAAAACTGAGATCTTGTTTTGACCAACAGAAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGATGTCTCTGTCAGGATCTAGTCCCATCCTG-AATCCATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTCAGAACTGACTGAATCAGGCCAGTGAAAGTTA-CAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATTGTGCATGGCTTCATTAGCAGGTTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCATCAGATTGTCAGGGTCTTGGATTCTGATAAGTTCTGTGTTCCTGATGAGAGACTGGTTATTCAGTAAGTTGTAGGACAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_awahnee_a"/>
-			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGAGAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_awahnee_b"/>
-			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGAKAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_xerophilus"/>
-			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCACTAAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTRTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_cactophilus"/>
-			C-AGCTTGCTG-TCACACTACCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCACTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCASTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_albatus"/>
-			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGTGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_ruidosae"/>
-			?????????????????????????????C-AGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_bottae"/>
-			C-AGCTTGCTG-TCACACYGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTAKGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCRTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_alpinus"/>
-			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCC-AGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGTTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCYACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_riparius"/>
-			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_mewa"/>
-			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAATTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_saxatilis"/>
-			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_laticeps"/>
-			C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_talpoides_ocius"/>
-			C-AGCTTGCTGGTCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCATATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAAWGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGACAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
-			C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTTTAAGTGTTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGTCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGTCCAGTGAAACTTAACAGCTACCTTGCCAATKGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGG--TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCGGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
-			CAAGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTGTTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGTCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGG--TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCGGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_mazama_mazama"/>
-			C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTATTGCCTGGATATAGTGTCTATAGACAGAGACAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCACATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCACCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAG-CGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_mazama_nasicus"/>
-			C-AGCTTGCTG-TCACAATGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTATTGCCTGGATATAGTGTCTATAGACAGAGACAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCACATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAG-CGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_monticola_a"/>
-			C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGACGCCKTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAGGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_monticola_b"/>
-			C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGACGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTYCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAGGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_talpoides_yakimensis"/>
-			C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGAMTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_talpoides_bridgeri"/>
-			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_townsendii_townsendii"/>
-			C-AGCTTGCTGGTCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_townsendii_relictus"/>
-			C-AGCTTGCTGGTCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_umbrinus_chihuahuae"/>
-			C-AGCTTGCTGGTCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAAGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTGGAATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGAGGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_umbrinus_atroavarius"/>
-			C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA
-		</sequence>
-	</alignment>
-
-	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
-	<!-- ntax=26 nchar=819                                                       -->
-	<alignment id="alignment3" dataType="nucleotide">
-		<sequence>
-			<taxon idref="Orthogeomys_heterodus"/>
-			CATGATTTTGTCATGCCTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGATGATTGACGCTGCTGTCAGTAGTGAGTGACACAAATTTTATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACGTGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAATTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATTTCTTTTCCA-CC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGATTTTATGGGACTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTAYCTGAAGGTTATTGATGGTGACCTCATTTTCTTGTGCTTGTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAATTCAGAGTTTGAACACTGTCCTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTCTATGTATGTGGTACCGTGCACTCAAACCCAGGTCTTTGTGAATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGCAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_awahnee_a"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACARAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGACGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_awahnee_b"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAMGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_xerophilus"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_cactophilus"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_albatus"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_ruidosae"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTYGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_bottae"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTYGTTTTCACCTGTGTGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCYGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGGTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAYGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_alpinus"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCYGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAYGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_riparius"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_mewa"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_saxatilis"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTARGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_bottae_laticeps"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_talpoides_ocius"/>
-			CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTATTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTT--------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTC-TATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATCTCTTTGTCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTGTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGTA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_idahoensis_pygmaeus_a"/>
-			???????TTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTCGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------T--GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGACTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTA--------CCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTA?????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_idahoensis_pygmaeus_b"/>
-			?ATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACTAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTATACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATGTTTTTTTT-G------------------------------CACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCACCACTTCTGGCTTTTTTTTTTCTACGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGCTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATTATGTTTGTGCAA????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_mazama_mazama"/>
-			??????????????????????A---GCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------------------------------------------------------------------------------TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAAGCACTTTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGTTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTT?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_mazama_nasicus"/>
-			??????????????GCTTTCTTACGTGCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCTTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAGGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTGTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTCC---------GGTACCATGCACTGGAACCCAGGTCTTCGTGCATGCTGGACAGCAACTCTACCACTAGGCAAAGCTTCTGGACCCATTAGT?????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_monticola_a"/>
-			CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGATCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_monticola_b"/>
-			CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAAYGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTT--GCCAGTCCTGGGCTTSAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTKTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGAYCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCYAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_talpoides_yakimensis"/>
-			?????????????????TTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGCTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAGTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------TTTGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCAGTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGTCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAATACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCAC???????????????????????????????????????????????????????
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_talpoides_bridgeri"/>
-			CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTCGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCYCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_townsendii_townsendii"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACACAAATTTCATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCCTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTT--ATATCATCTTTGTGCAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_townsendii_relictus"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_umbrinus_chihuahuae"/>
-			CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTRCCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A
-		</sequence>
-		<sequence>
-			<taxon idref="Thomomys_umbrinus_atroavarius"/>
-			CATGATTTTGTCATGYTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTYGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTTYATATCATCTTTGTGAAACT-A
-		</sequence>
-	</alignment>
-
-	<!-- The unique patterns from 1 to end                                       -->
-	<!-- npatterns=144                                                           -->
-	<patterns id="26.patterns" from="1">
-		<alignment idref="alignment1"/>
-	</patterns>
-
-	<!-- The unique patterns from 1 to end                                       -->
-	<!-- npatterns=71                                                            -->
-	<patterns id="29.patterns" from="1">
-		<alignment idref="alignment2"/>
-	</patterns>
-
-	<!-- The unique patterns from 1 to end                                       -->
-	<!-- npatterns=153                                                           -->
-	<patterns id="47.patterns" from="1">
-		<alignment idref="alignment3"/>
-	</patterns>
-
-	<!-- This is a simple constant population size coalescent model              -->
-	<!-- that is used to generate an initial tree for the chain.                 -->
-	<constantSize id="initialDemo" units="substitutions">
-		<populationSize>
-			<parameter id="initialDemo.popSize" value="100.0"/>
-		</populationSize>
-	</constantSize>
-
-	<!-- Generate a random starting tree under the coalescent process            -->
-	<coalescentTree id="26.startingTree" rootHeight="0.017">
-		<taxa idref="taxa"/>
-		<constantSize idref="initialDemo"/>
-	</coalescentTree>
-
-	<!-- Generate a random starting tree under the coalescent process            -->
-	<coalescentTree id="29.startingTree" rootHeight="0.016">
-		<taxa idref="taxa"/>
-		<constantSize idref="initialDemo"/>
-	</coalescentTree>
-
-	<!-- Generate a random starting tree under the coalescent process            -->
-	<coalescentTree id="47.startingTree" rootHeight="0.017">
-		<taxa idref="taxa"/>
-		<constantSize idref="initialDemo"/>
-	</coalescentTree>
-
-	<!-- Generate a tree model                                                   -->
-	<treeModel id="26.treeModel">
-		<coalescentTree idref="26.startingTree"/>
-		<rootHeight>
-			<parameter id="26.treeModel.rootHeight"/>
-		</rootHeight>
-		<nodeHeights internalNodes="true">
-			<parameter id="26.treeModel.internalNodeHeights"/>
-		</nodeHeights>
-		<nodeHeights internalNodes="true" rootNode="true">
-			<parameter id="26.treeModel.allInternalNodeHeights"/>
-		</nodeHeights>
-	</treeModel>
-
-	<!-- Generate a tree model                                                   -->
-	<treeModel id="29.treeModel">
-		<coalescentTree idref="29.startingTree"/>
-		<rootHeight>
-			<parameter id="29.treeModel.rootHeight"/>
-		</rootHeight>
-		<nodeHeights internalNodes="true">
-			<parameter id="29.treeModel.internalNodeHeights"/>
-		</nodeHeights>
-		<nodeHeights internalNodes="true" rootNode="true">
-			<parameter id="29.treeModel.allInternalNodeHeights"/>
-		</nodeHeights>
-	</treeModel>
-
-	<!-- Generate a tree model                                                   -->
-	<treeModel id="47.treeModel">
-		<coalescentTree idref="47.startingTree"/>
-		<rootHeight>
-			<parameter id="47.treeModel.rootHeight"/>
-		</rootHeight>
-		<nodeHeights internalNodes="true">
-			<parameter id="47.treeModel.internalNodeHeights"/>
-		</nodeHeights>
-		<nodeHeights internalNodes="true" rootNode="true">
-			<parameter id="47.treeModel.allInternalNodeHeights"/>
-		</nodeHeights>
-	</treeModel>
-
-	<!-- Generate a variableDemographic for extended Bayesian skyline process    -->
-	<variableDemographic id="demographic" type="linear" useMidpoints="true">
-		<populationSizes>
-
-			<!-- popSize value = populationMean value                                    -->
-			<parameter id="demographic.popSize" value="0.017"/>
-		</populationSizes>
-		<indicators>
-			<parameter id="demographic.indicators" value="0.0"/>
-		</indicators>
-		<trees>
-			<ptree ploidy="2.0">
-				<treeModel idref="26.treeModel"/>
-			</ptree>
-			<ptree ploidy="2.0">
-				<treeModel idref="29.treeModel"/>
-			</ptree>
-			<ptree ploidy="2.0">
-				<treeModel idref="47.treeModel"/>
-			</ptree>
-		</trees>
-	</variableDemographic>
-	<coalescentLikelihood id="coalescent">
-		<model>
-			<variableDemographic idref="demographic"/>
-		</model>
-
-		<!-- Take population Tree from demographic                                   -->
-	</coalescentLikelihood>
-	<sumStatistic id="demographic.populationSizeChanges" elementwise="true">
-		<parameter idref="demographic.indicators"/>
-	</sumStatistic>
-	<exponentialDistributionModel id="demographic.populationMeanDist">
-		<mean>
-
-			<!-- prefer populationMean value = 1                                         -->
-			<parameter id="demographic.populationMean" value="0.017"/>
-		</mean>
-	</exponentialDistributionModel>
-
-	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
-	<HKYModel id="26.hky">
-		<frequencies>
-			<frequencyModel dataType="nucleotide">
-				<frequencies>
-					<parameter id="26.frequencies" value="0.25 0.25 0.25 0.25"/>
-				</frequencies>
-			</frequencyModel>
-		</frequencies>
-		<kappa>
-			<parameter id="26.kappa" value="2.0" lower="0.0"/>
-		</kappa>
-	</HKYModel>
-
-	<!-- site model                                                              -->
-	<siteModel id="26.siteModel">
-		<substitutionModel>
-			<HKYModel idref="26.hky"/>
-		</substitutionModel>
-	</siteModel>
-
-	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
-	<HKYModel id="29.hky">
-		<frequencies>
-			<frequencyModel dataType="nucleotide">
-				<frequencies>
-					<parameter id="29.frequencies" value="0.25 0.25 0.25 0.25"/>
-				</frequencies>
-			</frequencyModel>
-		</frequencies>
-		<kappa>
-			<parameter id="29.kappa" value="2.0" lower="0.0"/>
-		</kappa>
-	</HKYModel>
-
-	<!-- site model                                                              -->
-	<siteModel id="29.siteModel">
-		<substitutionModel>
-			<HKYModel idref="29.hky"/>
-		</substitutionModel>
-	</siteModel>
-
-	<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
-	<HKYModel id="47.hky">
-		<frequencies>
-			<frequencyModel dataType="nucleotide">
-				<frequencies>
-					<parameter id="47.frequencies" value="0.25 0.25 0.25 0.25"/>
-				</frequencies>
-			</frequencyModel>
-		</frequencies>
-		<kappa>
-			<parameter id="47.kappa" value="2.0" lower="0.0"/>
-		</kappa>
-	</HKYModel>
-
-	<!-- site model                                                              -->
-	<siteModel id="47.siteModel">
-		<substitutionModel>
-			<HKYModel idref="47.hky"/>
-		</substitutionModel>
-	</siteModel>
-
-	<!-- Likelihood for tree given sequence data                                 -->
-	<treeLikelihood id="26.treeLikelihood" useAmbiguities="false">
-		<patterns idref="26.patterns"/>
-		<treeModel idref="26.treeModel"/>
-		<siteModel idref="26.siteModel"/>
-	</treeLikelihood>
-
-	<!-- Likelihood for tree given sequence data                                 -->
-	<treeLikelihood id="29.treeLikelihood" useAmbiguities="false">
-		<patterns idref="29.patterns"/>
-		<treeModel idref="29.treeModel"/>
-		<siteModel idref="29.siteModel"/>
-	</treeLikelihood>
-
-	<!-- Likelihood for tree given sequence data                                 -->
-	<treeLikelihood id="47.treeLikelihood" useAmbiguities="false">
-		<patterns idref="47.patterns"/>
-		<treeModel idref="47.treeModel"/>
-		<siteModel idref="47.siteModel"/>
-	</treeLikelihood>
-
-	<!-- Define operators                                                        -->
-	<operators id="operators">
-		<scaleOperator scaleFactor="0.75" weight="0.1">
-			<parameter idref="26.kappa"/>
-		</scaleOperator>
-		<deltaExchange delta="0.01" weight="0.1">
-			<parameter idref="26.frequencies"/>
-		</deltaExchange>
-		<scaleOperator scaleFactor="0.75" weight="0.1">
-			<parameter idref="29.kappa"/>
-		</scaleOperator>
-		<deltaExchange delta="0.01" weight="0.1">
-			<parameter idref="29.frequencies"/>
-		</deltaExchange>
-		<scaleOperator scaleFactor="0.75" weight="0.1">
-			<parameter idref="47.kappa"/>
-		</scaleOperator>
-		<deltaExchange delta="0.01" weight="0.1">
-			<parameter idref="47.frequencies"/>
-		</deltaExchange>
-		<upDownOperator scaleFactor="0.75" weight="30">
-			<up>
-			</up>
-			<down>
-				<parameter idref="demographic.populationMean"/>
-				<parameter idref="demographic.popSize"/>
-				<parameter idref="26.treeModel.allInternalNodeHeights"/>
-				<parameter idref="29.treeModel.allInternalNodeHeights"/>
-				<parameter idref="47.treeModel.allInternalNodeHeights"/>
-			</down>
-		</upDownOperator>
-		<subtreeSlide size="0.0017" gaussian="true" weight="15">
-			<treeModel idref="26.treeModel"/>
-		</subtreeSlide>
-		<narrowExchange weight="15">
-			<treeModel idref="26.treeModel"/>
-		</narrowExchange>
-		<wideExchange weight="3">
-			<treeModel idref="26.treeModel"/>
-		</wideExchange>
-		<wilsonBalding weight="3">
-			<treeModel idref="26.treeModel"/>
-		</wilsonBalding>
-		<scaleOperator scaleFactor="0.75" weight="3">
-			<parameter idref="26.treeModel.rootHeight"/>
-		</scaleOperator>
-		<uniformOperator weight="30">
-			<parameter idref="26.treeModel.internalNodeHeights"/>
-		</uniformOperator>
-		<subtreeSlide size="0.0016" gaussian="true" weight="15">
-			<treeModel idref="29.treeModel"/>
-		</subtreeSlide>
-		<narrowExchange weight="15">
-			<treeModel idref="29.treeModel"/>
-		</narrowExchange>
-		<wideExchange weight="3">
-			<treeModel idref="29.treeModel"/>
-		</wideExchange>
-		<wilsonBalding weight="3">
-			<treeModel idref="29.treeModel"/>
-		</wilsonBalding>
-		<scaleOperator scaleFactor="0.75" weight="3">
-			<parameter idref="29.treeModel.rootHeight"/>
-		</scaleOperator>
-		<uniformOperator weight="30">
-			<parameter idref="29.treeModel.internalNodeHeights"/>
-		</uniformOperator>
-		<subtreeSlide size="0.0017" gaussian="true" weight="15">
-			<treeModel idref="47.treeModel"/>
-		</subtreeSlide>
-		<narrowExchange weight="15">
-			<treeModel idref="47.treeModel"/>
-		</narrowExchange>
-		<wideExchange weight="3">
-			<treeModel idref="47.treeModel"/>
-		</wideExchange>
-		<wilsonBalding weight="3">
-			<treeModel idref="47.treeModel"/>
-		</wilsonBalding>
-		<scaleOperator scaleFactor="0.75" weight="3">
-			<parameter idref="47.treeModel.rootHeight"/>
-		</scaleOperator>
-		<uniformOperator weight="30">
-			<parameter idref="47.treeModel.internalNodeHeights"/>
-		</uniformOperator>
-		<scaleOperator scaleFactor="0.9" weight="3">
-			<parameter idref="demographic.populationMean"/>
-		</scaleOperator>
-		<sampleNonActiveOperator weight="15">
-			<distribution>
-				<parameter idref="demographic.populationMeanDist"/>
-			</distribution>
-			<data>
-				<parameter idref="demographic.popSize"/>
-			</data>
-			<indicators>
-				<parameter idref="demographic.indicators"/>
-			</indicators>
-		</sampleNonActiveOperator>
-		<bitFlipOperator weight="30">
-			<parameter idref="demographic.indicators"/>
-		</bitFlipOperator>
-		<scaleOperator scaleFactor="0.5" weight="6">
-			<parameter idref="demographic.popSize"/>
-			<indicators pickoneprob="1.0">
-				<parameter idref="demographic.indicators"/>
-			</indicators>
-		</scaleOperator>
-	</operators>
-
-	<!-- Define MCMC                                                             -->
-	<mcmc id="mcmc" chainLength="10000000" autoOptimize="true">
-		<posterior id="posterior">
-			<prior id="prior">
-				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
-					<parameter idref="26.kappa"/>
-				</logNormalPrior>
-				<uniformPrior lower="0.0" upper="1.0">
-					<parameter idref="26.frequencies"/>
-				</uniformPrior>
-				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
-					<parameter idref="29.kappa"/>
-				</logNormalPrior>
-				<uniformPrior lower="0.0" upper="1.0">
-					<parameter idref="29.frequencies"/>
-				</uniformPrior>
-				<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
-					<parameter idref="47.kappa"/>
-				</logNormalPrior>
-				<uniformPrior lower="0.0" upper="1.0">
-					<parameter idref="47.frequencies"/>
-				</uniformPrior>
-				<poissonPrior mean="0.6931471805599453" offset="0.0">
-					<statistic idref="demographic.populationSizeChanges"/>
-				</poissonPrior>
-				<oneOnXPrior>
-					<parameter idref="demographic.populationMean"/>
-				</oneOnXPrior>
-				<coalescentLikelihood idref="coalescent"/>
-				<mixedDistributionLikelihood>
-					<distribution0>
-						<exponentialDistributionModel idref="demographic.populationMeanDist"/>
-					</distribution0>
-					<distribution1>
-						<exponentialDistributionModel idref="demographic.populationMeanDist"/>
-					</distribution1>
-					<data>
-						<parameter idref="demographic.popSize"/>
-					</data>
-					<indicators>
-						<parameter idref="demographic.indicators"/>
-					</indicators>
-				</mixedDistributionLikelihood>
-			</prior>
-			<likelihood id="likelihood">
-				<treeLikelihood idref="26.treeLikelihood"/>
-				<treeLikelihood idref="29.treeLikelihood"/>
-				<treeLikelihood idref="47.treeLikelihood"/>
-			</likelihood>
-		</posterior>
-		<operators idref="operators"/>
-
-		<!-- write log to screen                                                     -->
-		<log id="screenLog" logEvery="100000">
-			<column label="Posterior" dp="4" width="12">
-				<posterior idref="posterior"/>
-			</column>
-			<column label="Prior" dp="4" width="12">
-				<prior idref="prior"/>
-			</column>
-			<column label="Likelihood" dp="4" width="12">
-				<likelihood idref="likelihood"/>
-			</column>
-			<column label="26.rootHeight" sf="6" width="12">
-				<parameter idref="26.treeModel.rootHeight"/>
-			</column>
-			<column label="29.rootHeight" sf="6" width="12">
-				<parameter idref="29.treeModel.rootHeight"/>
-			</column>
-			<column label="47.rootHeight" sf="6" width="12">
-				<parameter idref="47.treeModel.rootHeight"/>
-			</column>
-		</log>
-
-		<!-- write log to file                                                       -->
-		<log id="fileLog" logEvery="1000" fileName="testEBSP.log" overwrite="false">
-			<posterior idref="posterior"/>
-			<prior idref="prior"/>
-			<likelihood idref="likelihood"/>
-			<parameter idref="26.treeModel.rootHeight"/>
-			<parameter idref="29.treeModel.rootHeight"/>
-			<parameter idref="47.treeModel.rootHeight"/>
-			<sumStatistic idref="demographic.populationSizeChanges"/>
-			<parameter idref="demographic.populationMean"/>
-			<parameter idref="demographic.popSize"/>
-			<parameter idref="demographic.indicators"/>
-			<parameter idref="26.kappa"/>
-			<parameter idref="26.frequencies"/>
-			<parameter idref="29.kappa"/>
-			<parameter idref="29.frequencies"/>
-			<parameter idref="47.kappa"/>
-			<parameter idref="47.frequencies"/>
-			<treeLikelihood idref="26.treeLikelihood"/>
-			<treeLikelihood idref="29.treeLikelihood"/>
-			<treeLikelihood idref="47.treeLikelihood"/>
-			<coalescentLikelihood idref="coalescent"/>
-		</log>
-
-		<!-- write tree log to file
-		<logTree id="26.treeFileLog" logEvery="1000" nexusFormat="true" fileName="testEBSP.26.trees" sortTranslationTable="true">
-			<treeModel idref="26.treeModel"/>
-			<posterior idref="posterior"/>
-		</logTree>
-		<logTree id="29.treeFileLog" logEvery="1000" nexusFormat="true" fileName="testEBSP.29.trees" sortTranslationTable="true">
-			<treeModel idref="29.treeModel"/>
-			<posterior idref="posterior"/>
-		</logTree>
-		<logTree id="47.treeFileLog" logEvery="1000" nexusFormat="true" fileName="testEBSP.47.trees" sortTranslationTable="true">
-			<treeModel idref="47.treeModel"/>
-			<posterior idref="posterior"/>
-		</logTree>  -->
-	</mcmc>
-	<report>
-		<property name="timer">
-			<mcmc idref="mcmc"/>
-		</property>
-	</report>
-<!-- 	<VDAnalysis id="demographic.analysis" burnIn="0.1" useMidpoints="true">
-		<logFileName>
-			testEBSP.log
-		</logFileName>
-		<treeFileNames>
-			<treeOfLoci>
-				testEBSP.26.trees
-			</treeOfLoci>
-			<treeOfLoci>
-				testEBSP.29.trees
-			</treeOfLoci>
-			<treeOfLoci>
-				testEBSP.47.trees
-			</treeOfLoci>
-		</treeFileNames>
-		<populationModelType>
-			linear
-		</populationModelType>
-		<populationFirstColumn>
-			demographic.popSize1
-		</populationFirstColumn>
-		<indicatorsFirstColumn>
-			demographic.indicators1
-		</indicatorsFirstColumn>
-	</VDAnalysis>
-	<CSVexport fileName="testEBSP.csv" separator=",">
-		<columns>
-			<VDAnalysis idref="demographic.analysis"/>
-		</columns>
-	</CSVexport> -->
-</beast>
diff -Nru beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/testEBSP-b2.xml beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/testEBSP-b2.xml
--- beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/testEBSP-b2.xml	1970-01-01 00:00:00.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/testEBSP-b2.xml	2022-04-04 07:18:36.000000000 +0000
@@ -0,0 +1,384 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" required="" version="2.6">
+        
+    <data
+id="hcv"
+spec="Alignment"
+name="alignment">
+                            
+        <sequence id="seq_AF271825i_0800" spec="Sequence" taxon="AF271825i_0800" totalcount="4" value="CTCTTGGCACTTCTTTCGTGCTTGACTGTCCCCGCTTCGGCCATCAACTACCGCAATGCTTCGGGCGTCTACCACGTCACCAACGACTGCCCGAATTCAAGCATAGTGTTTGAGGCCGACCATCACATCTTACACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCTCGTTGCTGGGTGGCTCTTACTCCTACTGTCGCAGCGCCACACATCGGCGCGCCGCTTGAATCCTTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGCTTGTTCGGCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTCGGTCAGATGTTCTCTTTCCGACCACGACGCCACTGGACTACCCAGGACTGCAATTGTTCTATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271826i_0873" spec="Sequence" taxon="AF271826i_0873" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTACCACAATGTTTCGGGCATCTACCATGTCACCAATGACTGCCCAAATTCAAGCATAGTGTATGAGGCCGACCATCACATCCTACACCTCCCAGGTTGCGTGCCCTGCGTGAGGACGGGGAACCAGTCGCACTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGAGTCATGTGGATCTGATGGTAGGGGCTGCCACTGTTTGTTCAGCCCTTTATATCGGGGATTTGTGTGGCGGCTTGTTTTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACCACCCAGGATTGCAATTGTTCCATCTATACGGGGCACATTACT"/>
+                            
+        <sequence id="seq_AF271827i_0883" spec="Sequence" taxon="AF271827i_0883" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCACCTCGGCCATTAACTATCGCAATGCTTCGGGCGTTTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCACGCTGCTGGGTGGCCCTTACCCCCACCGTCGCAGCGCCATACATCGGCGCGCCACTTCAATCTCTACGGAGTCATGTGGATTTGATGGTGGGGGCCGCCACTGCTTGTTCAGCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTCGGTCAGATGTTCTCTTTCCGGCCACGGCGCCACTGGACTACCCAGGACTGCAATTGTTCCATCTATACAGGGCACATCATG"/>
+                            
+        <sequence id="seq_AF271828i_0922" spec="Sequence" taxon="AF271828i_0922" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTATCGCAATGTCTCGGGCATTTACCACATCACCAATGACTGCCCGAATTCAAGCATAGTGTTTGAGGCCGATCACCACATCTTACACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCGCGTTGCTGGGTGGCCCTAACTCCTACCGTCGCAGCGCCGTACATCGGCGCACCACTTGAGTCCTTACGGAGTCATGTGGATTTGATGGTGGGGGCTGCCACTGCTTGTTCGGCCCTTTACATCGGGGATTTGTGTGGTGGCTTGTTCCTGGTTGGTCAGATGTTCTCCTTCCGACCACGGCGCCACTGGACTACCCAGGAATGCAATTGCTCCATCTATTCAGGACACCTCACT"/>
+                            
+        <sequence id="seq_AF271829i_0923" spec="Sequence" taxon="AF271829i_0923" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCACCAACTACCACAATGCTTCGGGCGTCTACCATGTCACCAATGACTGCCCAAATTCAAGCATAGTGTTTGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCGCGCTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCTCTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGTCTGCTCAGCCTTTTACATCGGGGATTTGTGTGGTGGCGTGTTCTTGGTCGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACTACCCAAGACTGCAATTGTTCCATCTATGCAGGGCACATTACG"/>
+                            
+        <sequence id="seq_AF271830i_1150" spec="Sequence" taxon="AF271830i_1150" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCACTAACTATCGCAATGTCTCGGGTATCTATCATGTCACCAATGATTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGCTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGCCTCCCTGCGGAGTCATGTGGATCTGATGGTGGGGGCCGCCACTGCTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATTTTCACCTTCCGACCACGGCGCCACTGGACTACCCAGGAATGCAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271831i_1164" spec="Sequence" taxon="AF271831i_1164" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATCGCAATGCCTCGGGCATCTACCATGTCACCAATGATTGCCCGAATTCAAGCATAGTGTATGAGGCCGAATATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGCGATGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTTGCAGCGCCGTACGTTGGCGCGCCGCTTGAGTCCCTGCGGAGTCATGTGGATCTGATGGTGGGAGCTGCCACTGTTTGTTCAGCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTTGGTCAAATGTTCTCTTTCCAGCCACGGCGTCACTGGACTACCCAGGGTTGTAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271832i_1226" spec="Sequence" taxon="AF271832i_1226" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCTTCAACTACCGCAACATCTCGGGTATTTACCATGTCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATTTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGGGAGGGGAATCAGTCACGCTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGAGTCATGTGGATATGATGGTGGGGGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATCTGTGTGGCGGCTTGTTTTTGGTTGGTCAGATGTTTTCTTTCCGACCACGACGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATGCAGGGCATATCACT"/>
+                            
+        <sequence id="seq_AF271833i_1240" spec="Sequence" taxon="AF271833i_1240" totalcount="4" value="CTCTTGGCACTACTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAATTACCGCAATGCCTCGGGCGTCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCCTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGCTGCTGGGTGGCCCTTACTCCTACTGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCTTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTTTTGGCTGGTCAGATGTTTTCTTTCCGGCCACGGCTCCACTGGACCACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271834i_1339" spec="Sequence" taxon="AF271834i_1339" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTTCCCGCTTCGGCCGTTAACTACCGCGATGCTTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCCTGCATCTCCCGGGTTGCGTGCCCTGCGTGAGAGTTGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCATCGCATCGCCATACATCGGTGCGCCGCTTGAATCCCTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGTTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGTCACTGGACCACCCAGGATTGCAATTGTTCCATCTACACGGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271835i_1767" spec="Sequence" taxon="AF271835i_1767" totalcount="4" value="CTCTTGGCACTTCTTTCGTGCTTGACTGTCCCCGCTTCGGCCGTTAACTACCGCAATGTCTCGGGCATCTACTATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCACCACATCTTGCACTTGCCAGGCTGCGTGCCCTGCGTGCGGGTGGGGAACCAGTCACGTTGCTGGGTGGCTCTCACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCACTTGAGTCTTTACGGAGTCATGTGGATTTGATGGTGGGGGCTGCCACTGTTTGTTCAGCCCTCTACATCGGGGATTTGTGTGGTGGCCTGTTCCTGGTTGGTCAGATGTTTTCTTTCCAACCACGGCGCCACTGGACCACCCAAGACTGCAATTGTTCCATCTATACGGGGCATATTACC"/>
+                            
+        <sequence id="seq_AF271836i_1796" spec="Sequence" taxon="AF271836i_1796" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCTTCAACTACCGCAACATCTCGGGTATTTACCATGTCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATTTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGGGAGGGGAATCAGTCGCGCTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGAGTCACGTGGATATGATGGTGGGGGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATCTGTGTGGCGGCTTGTTTCTGGTTGGTCAGATGTTTTCTTTCCGACCACGACGCCACTGGACTACCCAGGAGTGCAATTGTTCCATCTATTCAGGGCATATCACT"/>
+                            
+        <sequence id="seq_AF271837i_1801" spec="Sequence" taxon="AF271837i_1801" totalcount="4" value="CTCTTGGCACTTCTCTCTTGTCTGACTGTCCCCGCTTCGGCCACTAACTACCGCAATGTTTCGGGCATCTACCACGTCACCAATGACTGCCCGAACTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGTGTGAGGACGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACCCCTACCGTCGCATCGCCATACATCGGCGCGCCACTTGCATCTCTACGGACTCATGTGGACTTGATGGTGGGGGCCGCCACTGTTTGTTCAGCCCTTTACATCGGAGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAAATGTTCTCTTTCCGACCAAGGCGCCACTGGACCACCCAGGATTGCAACTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271838i_1803" spec="Sequence" taxon="AF271838i_1803" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCACCAACTATCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGATCACCACATCTTGCACTTGCCAGGTTGCGTGCCCTGCGTGCAAACGGGGAATCAGTCACGTTGCTGGGTGGCCCTCACTCCTACCGTCGCAGCGCCGTATATCGGCGCGCCACTTGAGTCTTTACGGAGTCATGTGGATTTGATGGTGGGAGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGACTTGTGTGGCGGCCTGTTCCTGGTTGGTCAGATGTTCTCTTTCCGACCGCGGCGCCACTGGACCACCCAAGACTGCAATTGTTCCATCTACACAGGGCACATTACT"/>
+                            
+        <sequence id="seq_AF271839i_1997" spec="Sequence" taxon="AF271839i_1997" totalcount="4" value="CTCTTGGCACTTCTTTCGTGCCTGACTGTTCCCNCTTCGGCCACTAACTATCGCAATGTTTCGGGCATCTACCATGTTACCAACGACTGCCCGAATTCAAGCATAGTATATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGYGTGAAAGTCGGGAACCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGYGCTCCGCTTGAGTCCCTGCGGAATCATGTGGATYTGATGGTGGGGGCTGCCACTGTTTGTTCAGCCCTTTACATCGGRGAYTTGTGTGGCGGCTTGTTTTTGGTTGGTCAGATGTTTTCTTTTCGGCCACGACGCCACTGGACTACCCAAGACTGCAACTGTTCCATCTATACGGGACACATCATG"/>
+                            
+        <sequence id="seq_AF271840i_2130" spec="Sequence" taxon="AF271840i_2130" totalcount="4" value="CTTTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTATCGCAATGTCTCGGGCATCTACCACGTCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGGACGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCACTTGAGTCTCTACGGAGTCATGTGGATTTGATGGTGGGGGCTGCCACTGTTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCCTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACCACCCAGGATTGCAATTGTTCCATCTATACGGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271841i_2134" spec="Sequence" taxon="AF271841i_2134" totalcount="4" value="CTTCTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATAGCAACGTCTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGACCGAACATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGCGTGACGGGAATCAGTCGCGTTGCTGGGTGGCCCTTACCCCTACCGTCGCAGCGTCACGACTCGACGCGCCGCTTGAGTCCTTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGCTTGCTCAGCCCTTTACATCGGGGATTTGTGTGGCGGTCTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGCCCACGGCGCCTCTGGACTACCCAGGATTGCAATTGTTCCATTTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271842i_2141" spec="Sequence" taxon="AF271842i_2141" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCACTAACTACCGCAACGCTTCGGGCATCTACCATGTCACCAATGACTGCCCGAATGCGAGCATAGTGTATGAGGCCGACCATCACATCCTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAAAGGGGAATCAGTCAAGCTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCTTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGTCTGTTCAGCCCTCTACATCGGGGATTTGTGTGGCGGCGTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGACGCCACTGGACTACCCAGGATTGCAATTGTCCCATCTATACAGGGCCCATTACT"/>
+                            
+        <sequence id="seq_AF271843i_2147" spec="Sequence" taxon="AF271843i_2147" totalcount="4" value="CTCTTGGCACTCCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTATCACAACACCTCGGGCGTCTACCACGTCACCAATGACTGCCCGAATTCAAGCATAGTCTATGAGGCCGACCATCACATCTTGCATCTCCCAGGGTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCACGTTGCTGGGTGGCCCTCACCCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCTTGCGGAGTCACGTGGATCTGATGGTGGGGGCAGCTACTGTCTGCTCTGCCCTTTACATCGGGGATTTGTGTGGCGGCGTGTTCTTGGTTGGTCAGATGTCCTCTTTCCGACCACGGCGCCACTGGACTACCCAGGAGTGCAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271844i_2150" spec="Sequence" taxon="AF271844i_2150" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGAGTGTCCCCGCCTCGGCAATTAATTACCGCAATGCTTCGGGTGTCTACCACGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCATCTTCCAGGCTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCCACCGTCGCGACGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGATTCATGTGGATCTGATGGTGGGGGCTGCCATTGCTTGTTCACCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTCGGTCAGATGTTCTCTTCCCGACCAAGGCTTCACTGGACTACTCAGGATCGCCATTGTTCCATCTATACGGGGCACATCTCC"/>
+                            
+        <sequence id="seq_AF271845i_2386" spec="Sequence" taxon="AF271845i_2386" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTACCGCAATGCTTCGGGCGTTTACCACATCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCATGCACCTTCCAGGTTGCGTGCCCTGCGTGAGGACGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGTGCCGTATATTGGCGCGCCACTTGACTCTCTTCGGAGTCATGTGGATTTGATGGTGGGGGCTGCTGCTGCTTGTTCAGCCCTTTACGTCGGGGACTTGTGTGGTGGCGTGTTCCTGGTCGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACTACCCAGGACTGCAACTGTTCCATCTACACAGGGCACATTACT"/>
+                            
+        <sequence id="seq_AF271846i_2429" spec="Sequence" taxon="AF271846i_2429" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTACCGCAATGTCTCGGGCATTTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGTTGCTGGGTGGCCCTAACTCCTACCGTCGCGGCACCACACATCGGTGCGCCACTTGAGTCTCTACGGAGTCATGTGGATTTGATGGTGGGGACCGCCACTGTTTGTTCAGCCCTTTACATCGGGGATTTATGTGGTGGTTTGTTCCTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGTCACTGGACCACCCAGGATTGCAATTGTTCCATCTACACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271847i_2438" spec="Sequence" taxon="AF271847i_2438" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCTGTCAACTACCGCAAYGCTTCGGGCGTTTACCATATCACCAATGAYTGTCCGAATGGAAGCATAGTGTATGAGGCCGACCATCACATYTTGCACCTCCCAGGTTGCGTGCCCTGCGTGAGARAGGGGAATCAGTCACGTTGCTGGGTAGCCCTTACTCCTACCMTCGCGGCGCCACACATCGGCGCGCCACTTGAATCTCTACGGAAACATGTGGATTTGAKGGTGGGAGCTGCTACWGCCTGTTCAGCCCTTTACATCGGGGATTTGTGTGCCGGCTTGTTCTTGGTCGGTCAGATGTTATCATTCCGACCACGACGCCACTGGACTACCCAGGATTGCAGTTGTTCCATCTAAACAGGACGAAGTGTT"/>
+                            
+        <sequence id="seq_AF271848i_2446" spec="Sequence" taxon="AF271848i_2446" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATCGCAATGCCTCGGGCATCTATCACGTCACCAATGACTGCCCGAATTCGAGCATAGTGTATGAGGCCGACAACCACATCCTGCACCTTCCAGGTTGCGTGCCCTGTGTGAAAGAGGGGAATCAGTCACGTTGCTGGGTGTCCCTTACTCCCACCGTCGCAGCGCCATACATCGGCGCGCCACTTGCGTCTCTACGGAGTCACGTGGATTTGATGGTGGGGGCTGCCACTGTTTGTTCAGCCCTCTACATCGGGGACTTGTGCGGCGGCTTGTTCTTGGTTGGCCAGATGTTCTCTTTCCAACCACGGCGTCACTGGACCACCCAGGATTGTAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271849i_2663" spec="Sequence" taxon="AF271849i_2663" totalcount="4" value="CTCTTAGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCGTTAACTACCGCAATGCTTCGGGTGTCTATCATATCACCAATGATTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCATGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGGGAACCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCATYGCAGCGCCATACATCGGCGCGTCGCTCGAGTCCTTGCGGAGTCATGTGGATGTGATGGTGGGGGCYGCCACTGTTTGTTCAGCCCTTTACATCGGGGACTTGTGTGGTGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCRCGGCGCCACTGGACTACCCAGGACTGCAACTGTTCCATTTATACAGGGCAGATACTG"/>
+                            
+        <sequence id="seq_AF271850i_2673" spec="Sequence" taxon="AF271850i_2673" totalcount="4" value="CTTTTGGCACTTCTCTCGTGCCTGACCGTCCCCGCTTCGGCCACCAACTATCGCAATGTCTCGGGCGTCTACCACATCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAAAGAGGGGAACCGGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACCTTGGCGCGCCACTTGAGTCTTTACGGAGCCATGTGGACTTGATGGTGGGAGCTGCCACTGCTTGTTCAGCCCTTTACATCGGAGACTTGTGTGGTGGCTTGTTCCTGGTTGGTCAGATGTTCTCTTTCCGACCACGACGCCACTGGACTACCCAAGAATGCAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271851i_2681" spec="Sequence" taxon="AF271851i_2681" totalcount="4" value="CTCTTGSCACTTCTCTCGTGCCTGACTGTCCCCACTTCGGCCATTAACTACCATAATGTTTCGGGCATCTATCACGTCACCAATGATTGTCCGAATTCAAGCATTGTGTATGAGGCCGATCATCACATCTTGCACGTTCCAGGCTGTGTGCCCTGCGTGAGAGAGGGAAATCAGTCACGTTGCTGGGTGGCCATTACTCCTACCCTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCCTGCGGAGTCACGTGGATMTGATGGTGGGGGCTGCCACTGCTTGNTCAGCCCTTTACATCGGGGATTTGTGTGCCGGTCTGTTCTTGGTTGGTCAGATGTTATCTTTCCGACCACGGCGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGAGCGNGTGTT"/>
+                            
+        <sequence id="seq_AF271852i_2685" spec="Sequence" taxon="AF271852i_2685" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCTTGACTGTCCCCGCTTCGGCCATTAACTACCGCAATGCGTCGGGCATCTACCATGTCACCAATGATTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGTGTGAGAGTGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCCACCGTCGCAGCGCCATACATCGGCGCGTCACTTGCATCTTTGCGGAGTCATGTGGATCTGATGGTGGGGACCGCCACTGTTTGTTCAGCCCTCTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCAACCACGGCGCCACTGGACTACCCAGGATTGCAATTGTTCTATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271853i_2852" spec="Sequence" taxon="AF271853i_2852" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTACCACAATGTCTCGGGCATCTACCATGTCACCAATGATTGCCCGAACTCAAGCATAGTGTATGAGGCCGAGCACCACATCCTGCACCTTCCTGGTTGCGTGCCCTGCGTGAGAGTGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGACTCCTTGCGGAGTCATGTGGATTTGATGGTGGGAACCGCCACTGTTTGTTCAGCTCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTTTCTTTTCAACCACGGCGCCATTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGACACATCACT"/>
+                            
+        <sequence id="seq_AF271854i_2856" spec="Sequence" taxon="AF271854i_2856" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCTGCTTCGGCCATCAATTACCGCAATGCCTCGGGCGTTTACCACATCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCATCTTCCAGGTTGCGTGCCCTGCGTAAGAGTGGGGAATCAGTCACGCTGCTGGGTGTCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCACCACTTGAGTCTCTACGGAGTCATGTAGACTTGATGGTGGGAGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTTCTGGTCGGTCAGATGTTCTCTTTCCGACCGCGACGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271855i_2862" spec="Sequence" taxon="AF271855i_2862" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCYATCAACTACCGCAATGCYTCGGGCGTCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCAYATCTTGCACCTTCCAGGATGCGTGCCCTGCGTGAAAGTGGGAAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATATRTTGGCGCGCCGCTTGAGTCCYTGCGGAGTCATGTGGACCTGATGGTGGGAGCTGCTACTGTCTGCTCAGCCCTTTACATTGGGGATTTGTGTGGCGGCGTGTTCTTGGTCGGCCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACTACCCAGGAGTGCAATTGTTCCATCTATACAGGGCAACTTACT"/>
+                            
+        <sequence id="seq_AF271856i_2926" spec="Sequence" taxon="AF271856i_2926" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATTAACTATCGCAATGTTTCGGGCGTCTACCACGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGAGCATCACATCTTGCACCTCCCAGGTTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCAAGTTGCTGGATGGCCCTTACCCCTACTGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCTTGCGGAGTCATGTGGATCTGATGGTGGGGGCCGCCACTGTTTGTTCAGCCCTTTACATCGGCGATCTGTGTGGCGGCTTGTTCTTGGTTGGCCAAATGTTCTCTTTCCAACCGCGGCGCCACTGGACCACCCAGGAGTGCAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271857i_2957" spec="Sequence" taxon="AF271857i_2957" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCRTCAACTACCGCAAYGTCTCGGGCATCTACCATGTCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCAYCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAAACAGGGGAATCAGTCACGTTGCTGGGTGGCCCTCACYCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCCTGCGGAGTCATGTGGATTTRATGGTGGGAGCTGCCACTGTTTGTTCAGCCTTTTACATCGGCGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTCTCMTTCCGACCACGGCGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCATG"/>
+                            
+        <sequence id="seq_AF271858i_3318" spec="Sequence" taxon="AF271858i_3318" totalcount="4" value="CTCTTGGCACTTCTCTCATGCCTGACTGTCCCTGCTTCGGCTATTAACTATCGCAATGYTTCGGGCATTTACCAYGTCACCAATGACTGTCCGAATTCTAGCATAGTGTATGAGGCCGATCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAAGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCATCGCAGCGCCATTCATCGGCGCGCCGCTTGAGTCTCTGMGGAGTCATGTGGAYTTGATGGTGGGGGCTGCYACTGCTTGTTCGGCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACKACCCAGGACTGTAAYTGKTCCATCTATACAGGGCACATTACT"/>
+                            
+        <sequence id="seq_AF271859i_3393" spec="Sequence" taxon="AF271859i_3393" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTACCGCAATGCTTCGGGCATCTACCATATCACCAATGATTGCCCGAATTCAAGCATAGTGTATGAGGCCGATCACCACATCTTGCACCTTCCAGGCTGCGTGCCCTGCGTGAGATCGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCGGCGCCACACATCGGCGCRCCGCTTGAGTCCTTGCGGAGTCAYGTGGATCTGATGGTGGGAACTGCCACTGTTTGTTCAGCCCTTTACATCGGCGATTTGTGTGGYGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCGCGGCGCCACTGGACTACCCAGGATTGCAACTGTTCCATCTATACAGGGCACATYACT"/>
+                            
+        <sequence id="seq_AF271860i_3400" spec="Sequence" taxon="AF271860i_3400" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATCGCAATGCTTCGGGTATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTACGAGGCCGACCACCACATTTTACACCTTCCAGGTTGCGTGCCCTGCGTGAGAGAGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGAGTCATGTGGATTTGATGGTGGGGGCTGCCACTGTCTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGTGTGTTCTTGGTCGGTCAGATGTTTTCTTTCCGACCACGACGCCACTGGACTACCCAGGATTGCAATTGCTCCATCTATACAGGGCACATCATG"/>
+                            
+        <sequence id="seq_AF271861i_3452" spec="Sequence" taxon="AF271861i_3452" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCCTCGGCCACTAATTACCGCAATGCTTCGGGTGTCTACCACGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCATCTTCCAGGCTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGWTGCTGGGTGGCCCTTACTCCCACCGTCGCGACGCCATACATCGGCGCACCGSTTGAGTCCCTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGYTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGWTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCTTCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271862i_3458" spec="Sequence" taxon="AF271862i_3458" totalcount="4" value="CTCTTGGCACTTCTTTCGTGCCTGACTGTCCCCGCTTCGGCCACCAACTACCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCCTGCACCTTCCAGGTTGCGTGCCTTGCGTGAGGGTGGGGAATCAGTCACGTTGCTGGGTGGCTCTTACCCCTACTGTCGCAGCGCCACACATCGGCGCGCCACTTGAGTCCTTGCGGAGTCATGTGGACTTGATGGTGGGGACTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGTGGCTTGTTTTTGGTTGGTCAGATGTTCTCTTTCCGACCGCGGCGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTACACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271863i_3460" spec="Sequence" taxon="AF271863i_3460" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCACCTCGGCCATCAACTATCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGTCCGAACTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCATCTCCCAGGWTGCGTGCCCTGTGTGAGAGTGGGGAATGTGTCAAGMTGTTGGGTGGCCCTTACCCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCTCTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATTTATGTGGCGGCTTGTTTTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271864i_3461" spec="Sequence" taxon="AF271864i_3461" totalcount="4" value="CTCTTGGCACTTCTTTCGTGCCTGACTGTCCCCGCTTCGGCCACCAATTACCGCAATGCCTCGGGCATCTACCATGTTACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCATATCTTNCACCTTCCAGGTTGCGTGCCCTGTGTGAGAGTGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACCCCTACCGTCGCAGCGCCATACATCGGCGCGCCACTTGAGTCCTTGCGGAGTCATGTGGACCTGATGGTGGGGACTGCCACTGTTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTTTTGGTTGGTCAGATGTTCTCTTTCCGACCGCGGCGCCACTGGACCACCCAGGATTGCAATTGTTCCATCTATACAGGACACATCACT"/>
+                            
+        <sequence id="seq_AF271865i_3463" spec="Sequence" taxon="AF271865i_3463" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCCTCGGCCGTTAACTACCACAATGTCTCGGGCATTTACCACGTCACCAACGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCACCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGGGTGGGGAATCAATCACGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACGTTGGCGCGCCACTTGAGTCTTTGCGGAGTCATGTGGATTTGATGGTGGGGGCTGCCACTGTTTGCTCAGCCCTTTACATCGGGGATTTATGCGGTGGTTTGTTCCTGGTCGGTCAGATGTTTTCTTTCCGGCCACGGCGCCACTGGACCACCCAGGATTGCAACTGTTCCATCTATACAGGGCACATCATG"/>
+                            
+        <sequence id="seq_AF271866i_3465" spec="Sequence" taxon="AF271866i_3465" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCTTGACTGTCCCCGCTTCGGCCACCAACTATCGCAACGCTTCGGGCGTCTACCATGTCACCAATGACTGCCCGAACTCAAGCATAGTGTATGAGGCCGACTATCACATCCTACACCTCCCAGGTTGTGTGCCTTGTGTGAAAACAGGGAACCAGTCACGTTGTTGGGTGGCCCTTACTCCTACTGTCGCAGCGCCATACATCGGTGCGCCGCTTGAGTCCTTACGGAGTCATGTGGATCTGATGGTGGGGGCAGCCGCCGCTTGTTCAGCCCTTTATGTCGGGGACCTGTGCGGCGGCGTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGTCACTGGACTACCCAGGATTGCAATTGTTCTATCTACACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271867i_3468" spec="Sequence" taxon="AF271867i_3468" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCTATCAACTACCATAATGCCTCGGGCATCTACCATGTCACCAAYGATTGCCCGAATGCAAGCATAGTGTATGAGGCCGACCACCACATCTTGCACCTTCCAGGTTGCTTGCCCTGTGTGAGAGTGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACCCCTACCGTTGCAGCGCCATACATCGGCGCACCGCTTGAGTCCTTGCGGAGTCATGTGGATCTAATGGTGGGGGCTGCCACTGCYTGTTCAGCCCTCTACATCGGAGACTTGTGCGGCGGCCTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCGCGACGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATTACT"/>
+                            
+        <sequence id="seq_AF271868i_3471" spec="Sequence" taxon="AF271868i_3471" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCACTTCGGCTATCAGCTATCGCAATGTCTCGGGCATTTATCACATCACCAACGACTGCCCGAATTCAAGCATAGTATATGAGGCCGACCATCACATCTTGCACTTTCCAGGTTGCGTGCCCTGTGTGAGAGAGGGGAATCAGTCGCGTTGCTGGGTGGCCCTTACCCCTACCGTCGCAGCGCCATACATCGGCGCGCCACTTGAGTCCCTACGGGGTCATGTGGATTTGATGGTGGGGACCGCCACTRTTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTATTCCTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACCACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACC"/>
+                            
+        <sequence id="seq_AF271869i_4020" spec="Sequence" taxon="AF271869i_4020" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGCCCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGAGAATCAGTCTCGCTGCTGGGTGGCCCTCACTCCTACCGTCGCAGCGCCATATATCGGCGCGCCGCTTGATTCCCTGCGGAGTCATGTGGATCTGATGGTGGGAGCTGCCACTGCTTGTTCGGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTTTCTTTCAGACCACGGCGCCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271870i_4033" spec="Sequence" taxon="AF271870i_4033" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCCTCGGCCACTAATTACCGCAATGCTTCGGGTGTCTACCACGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCATCTTCCAGGCTGCGTGCCCTGCGTGAGAACGGGGAATCAGTCACGTTGCTGGGTGGCCCTTACTCCCACCGTCGCGACGCCATACATCGGCGCACCGCTTGAGTCCCTGCGGAGTCATGTGGATCTGATGGTGGGGGCTGCCACTGCTTGTTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCTTCACTGGACTACCCAGGATTGCAATTGTTCCATCTATACAGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271871i_4036" spec="Sequence" taxon="AF271871i_4036" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTCCCCGCTTCGGCCATCAACTATCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGCCCATCACATCTTGCACCTTCCAGGTTGCGTGCCCTGCGTGAGAACGGAGAATCAGTCTCGCTGCTGGGTGGCCCTCACTCCTACCGTCGCAGCGCCATATATCGGCGCGCCGCTTGATTCCCTGCGGAGTCATGTGGATCTGATGGTGGGAGCTGCCACTGCTTGTTCGGCCCTTTACATCGGGGATTTGTGTGGCGGCTTGTTCTTGGTTGGTCAAATTTTTCCTTTCAGACCACGGCGCCACTGGAATACCCAGGAATTGCATTGTTCCATCTATACAGGGCACATCACG"/>
+                            
+        <sequence id="seq_AF271872i_4053" spec="Sequence" taxon="AF271872i_4053" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACTGTTCCCGCTTCGGCCATCAACTACCGCAATGTCTCGGGCATCTACCATGTCACCAATGACTGCCCAAATTCAAGCATAGTATATGAGGCCGACCATCACATCCTGCACCTTCCGGGTTGTGTGCCCTGTGTGAGGGAGGGGAATCAGTCGCGTTGCTGGGTGGCCCTTACTCCTACCGTCGCAGCGCCATACATCGGCGCGCCGCTTGAGTCCCTGCGGAGTCACGTGGATCTGATGGTGGGAGCCGCTACTGTTTGCTCACCCCTTTACATCGGGGACTTGTGTGGCGGCTTGTTCTTGGTTGGTCAAATGTTCTCTTTCCGACCACGGCGTCACTGGACTACTCAGGAATGCAATTGTTCCATCTACGCGGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271873i_4055" spec="Sequence" taxon="AF271873i_4055" totalcount="4" value="CTCTCGGCACTTCTCTCGTGCTTGACTGTCCCCGCTTCGGCCGTCAACTATCGCAACATCTCGGGCGTCTACCATGTCACCAATGACTGCCCGAATTCAAGCATAGTGTATGAGGCCGACCATCACATCTTGCACCTCCCAGGTTGTGTGCCCTGCGTGAGAGTGGGGAATCAGTCGCGTTGCTGGGTGGCCCTTACCCCTACCGTCGCAGCGCCATACATTGGCGCGCCGCTTGACTCCCTGCGGAGTCACGTGGATCTGATGGTGGGAGCAGCCACTGTTTGCTCAGCCCTTTACATCGGGGATTTGTGTGGCGGCGCCTTCTTGGTTGGTCAGATGTTCTCTTTCCGACCACGGCGCCACTGGACTACCCAGGATCGCAATTGTCCCATCTACACTGGGCACATCACT"/>
+                            
+        <sequence id="seq_AF271874i_1359" spec="Sequence" taxon="AF271874i_1359" totalcount="4" value="CTTTTGGCACTTCTCTCGTGCCTGACTGTTCCTGCATCAGCCATTCACTATCGCAACAGTTCGGGCATCTACCACATCACCAACGATTGCCCAAATTCTAGCATAGTTTATGATTCTGACCATCACATCCTACACCTCCCAGGATGCGTACCCTGTGTGAGGAGCGGGAACATGTCGCGATGCTGGGTGTCCTTAACCCCCACCGTGGCAGCGCCGTATCCCAACGCACCACTTCAGTCCTTGCGACGGCATGTAGACCTGATGGTGGGCGCTGCTACCATGTGTTCAGCCTTCTACGTCGGCGACCTGTGTGGGGGCCTATTTTTGATAGGCCAGGCCTTTAATTTCCAACCACGCCGCCACTGGACTACTCAGGATTGCAATTGCTCCATCTATACAGGCCACATCACA"/>
+                            
+        <sequence id="seq_AF271875i_1380" spec="Sequence" taxon="AF271875i_1380" totalcount="4" value="CTCTTGGCACTCCTCTCGTGCCTGACTGTCCCCGCATCGGCCGCACATTATCGCAATGCTTCGGGTGTCTACCATATCACCAATGACTGCCCGAATTCTAGCATAGTGTACGAGGCTGATCACCACATCATGCACCTTCCGGGGTGCGTGCCCTGCGTCAAGACCGGCAACGTATCGCGGTGTTGGGTAGCTTTGACCCCCACTGTGGCGGCCCCCTACCTCAATGCTCCAACAGAAGCGCTTAGGCGCCATGTGGACTTGATGGTGGGTGCCGCCACTTTCTGCTCCGCCCTTTACATCGGCGATTTGTGTGGGGGAGCCTTCTTAGTGGGCCAACTATTCACATTCCGGCCGCGTCGCCATTGGACCACGCAGGACTGCAACTGCTCCATCTACACCGGTCACATCACA"/>
+                            
+        <sequence id="seq_AF271876i_1797" spec="Sequence" taxon="AF271876i_1797" totalcount="4" value="CTCTTGGCACTCCTCTCGTGCCTGACTGTCCCCGCATCAGCCACGCATTATCGCAATGCTTCGGGCGTCTACCACATCACCAACGACTGCCCGAATTCCAGCATAGTGTACGAGGGTCAGCATCACATCCTGCACCTTCCCGGGTGTGTACCCTGTGTCAAAACCGACAACGTATCGCGGTGTTGGGTAGCTTTGACCCCCACTGTGGCGGCTCCCTACCTCAATGCTCCAACAGAAGAGCTCAGGCACCATGTGGACATGCTGGTGGGTGCCGCTACTTTTTGCTCCGCCCTTTACATCGGCGACTTGTGTGGGGGAGCCTTCTTAGTGGGCCAGCTATTCACATTCCGGCCGCGTCGCCATTGGACCACGCAGGATTGCAACTGTTCCATCTACGCTGGTCACATCACA"/>
+                            
+        <sequence id="seq_AF271877i_1999" spec="Sequence" taxon="AF271877i_1999" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACCGTCCCCGCATCGGCCATACACTATCATAACACCTCGGGCATCTATCACATCACCAATGATTGCCCAAATTCCAGCATAGTTTATGAGTCCAGCAACCACATAATGCACCTTCCGGGGTGTGTACCATGTGTGAGGAGCGGGAACGTGTCGAGGTGTTGGGTGGCTTTAACTCCCACAGTGGCGGCCCCATACGTCGGTGCTCCAGTTGAGTCTCTACGACGACATGTGGACCTGATGGTGGGTGCTGCCACTTTGTGCTCCGCCCTATATGTCGGGGACCTGTGCGGAGGTGTGTTTCTGGTGGGTCAGATGTTCACCTTCCGCCCCCGCCTCCACTGAACTACTCAAGACTGTAACTGTTCAATCTATTCTGGGCATGTCACG"/>
+                            
+        <sequence id="seq_AF271878i_2000" spec="Sequence" taxon="AF271878i_2000" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACCGTCCCCGCATCGGCCATACACTATCATAACACCTCGGGCATCTATCACATCACCAATGATTGCCCAAATTCCAGCATAGTTTATGAGTCCAGCAACCACATAATGCACCTTCCGGGGTGTGTACCATGTGTGAGGAGCGGGAACGTGTCGAGCTGTTGGGTGGCTTTAACTCCCACAGTGGCGGCCCCATACGTCGGTGCTCCAGTTGAGTCTCTACGACGACACGTGGACCTGATGGTGGGTGCTGCCACTTTGTGCTCCGCCCTATATGTCGGGGACCTGTGCGGAGGTGTGTTTCTGGTGGGTCAGATGTTCACCTTCCGCCCCCGCCTCCACTGGACTACTCAAGACTGTAACTGTTCAATCTATTCTGGGCATGTCACG"/>
+                            
+        <sequence id="seq_AF271879i_2113" spec="Sequence" taxon="AF271879i_2113" totalcount="4" value="CTTTTGGCACTTCTCTCGTGCCTGACCGTCCCCACGTCGGCCATACACTATCATAACACCTCGGGCATCTATCACATCACCAACGATTGCCCAAATTCCAGCATAGTTTATGAGTCCGACTACCACATAGTGCACCTTCCGGGGTGCGTACCATGTGTGAGAACCGGAAACGCGTCGACGTGTTGGGTGGCCTTGTCTCCCACAGTGGCGGCCCCATACATCGGTGCTCCAGTTGAGTCTCTACGGCGACACGTGGACCTGATGGTGGGAGCTGCCACCTTGTGCTCTGCCCTATATGTCGGGGACCTGTGCGGAGGTGCGTTTCTGGTCGGCCAGATGTTCACCTTCCGCCCTCGTCTCCACTGGACCACCCAGGACTGCAACTGTTCAATCTACTCTGGGCATATCACG"/>
+                            
+        <sequence id="seq_AF271880i_2115" spec="Sequence" taxon="AF271880i_2115" totalcount="4" value="CTCTTGGCACTCCTTTCATGCCTGACCGTTCCCGCCTCGGCCATACACTATCGCAATGCTTCGGACGTCTACCACATCACCAACGACTGTCCGAATTCCAGCATAGTCTATGAATCCGAGAATCACATCTTACACCTTCCGGGGTGCGTACCCTGTGTGAAGGTCGGGAATAGGTCACAATGCTGGGTGGCCCTAACCCCCACCGTGGCGGCGTCGTACCTCAATGCTCCAATCGACTCCTTACGGAAGCACGTGGACCTGATGGTTGGCGCCGCTACTGTGTGCTCAGCTCTCTATGTTGGAGACGTGTGCGGGGCTGTGTTCCTGGCGGGCCAGATGGTGACGTTTCGACCGCGGCGCCACTGGACCACTCAGGAGTGCAACTGTTCCATCTATGCTGGGCACGTCACA"/>
+                            
+        <sequence id="seq_AF271881i_2116" spec="Sequence" taxon="AF271881i_2116" totalcount="4" value="CTCTTGGCACTCCTTTCATGCCTGACCGTTCCCGCCTCGGCCATACACTATCGCAATGCTTCGGACGTCTACCACATCACCAACGACTGTCCGAATTCCAGCATAGTCTATGAATCCGAGAATCACATCTTACACCTTCCGGGGTGCGTACCCTGTGTGAAGGTCGGGAATAGGTCACAATGCTGGGTGGCCCTAACCCCCACCGTGGCGGCGTCGTACCTCAATGCTCCAATCGACTCCTTACGGAAGCACGTGGACCTGATGGTTGGCGCCGCTACTGTGTGCTCAGCTCTCTATGTTGGAAACGTGTGCGGGGCTGTGTTCCTGGCGGGCCAGATGGTGACGTTTCGACCGCGGCGCCACTGGACCACTCAGGAGTGCAACTGTTCCATCTATGCTGGGCACCTCACA"/>
+                            
+        <sequence id="seq_AF271882i_2153" spec="Sequence" taxon="AF271882i_2153" totalcount="4" value="CTTCTGGCACTCCTCTCGTGCCTGACCGTCCCCGCATCGGCCATACACTATCATAACACCTCGGGCATCTACCACATCACCAATGATTGCCCAAATTCCAGCATAGTCTATGAGTCCGATCATCACATAATGCACCTTCCGGGGTGCGTGCCATGTGTGATGGAAGGGAACAGATCCAGGTGTTGGGTGGCCCTGTCTCCCACAGTGGCGACCTCACACGTTGGTGCTCCAGTTGAGTCCATGCGACGACATGTGGACCTGATGGTGGGCGCTGCCACTTTGTGCTCCGCCCTATACGTCGGGGACTTGTGCGGAGGTGTGTTTCTGGTTGGTCAGATGTTCACCTTTCAGCCTCGTCGCCACTGGACTACCCAGGACTGCAACTGCTCAATCTATTCTGGGCATGTCACG"/>
+                            
+        <sequence id="seq_AF271883i_2432" spec="Sequence" taxon="AF271883i_2432" totalcount="4" value="CTTTTGGCACTTCTTTCGTGCCTGACCGTTCCTGCATCAGCCACTCACTATCGCAATAGTTCGGGTGTCTACCACATCACTAATGACTGCCCGAATTCCAGCATAGTTTATGAGGCTGACCATCACATCTTACACCTCCCAGGATGCTTGCCCTGTGTGAAGAGCGGGAACGTGTCGCGATGCTGGGTGTCCTTAACCCCCACCGTGGCAGCGCCGCATCATAACGCACCACTTRAGTCCTTGCGACGGCATGTGGACCTGATGGTGGGCGCTGCTACCATGTGTTCTGCCCTCTACATCGGCGACTTGTGCGGGGGCTTGTTTCTGATAGGCCAGGCCTTTASTTTCCAACCGCGCCGCCACTGGACTACTCAGGATTGTAATTGCTCCATCTATACAGGCCACATTACA"/>
+                            
+        <sequence id="seq_AF271884i_2659" spec="Sequence" taxon="AF271884i_2659" totalcount="4" value="CTTTTGGCACTTCTCTCGTGCCTGACCGTTCCTGCATCAGCCATTCACTATCGCAACAGTTCGGGCGTCTACCACGTCACCAATGACTGCCCCAATTCCAGCATAGTTTATGAGGCTGACCATCACATCCTACACCTCCCAGGATGCGTGCCCTGTGTGAGGAGCGGGAACGTGTCGCGATGCTGGGTGTCCTTAACCCCCACCGTGGCGGCGCCATACCTCAATGCGCCACTTCAGTCCTTGCGACGGCATGTGGACCTGATGGTGGGCGCTGCTACCATGTGTTCTGCCCTTTACATCGGCGACTTGTGTGGGGGCCTGTTTCTGATAGGCCAGGCCTTTACTTTCCAACCACGCCGCCACTGGACTACTCAGGATTGCAATTGCTCCATCTATTCAGGCCACATCACA"/>
+                            
+        <sequence id="seq_AF271885i_3289" spec="Sequence" taxon="AF271885i_3289" totalcount="4" value="CTTTTGGCACTTCTCTCGTGCCTGACCGTTCCCGCATCAGCCATTCACTATCGCAACAGCTCGGGCATCTACCACATCACCAATGACTGCCCCAACTCCAGCATAATTTATGAGGCTGACCATCACATCCTACACCTCCCAGGATGCGTGCCCTGTGTGAGGAGCGGGAACGTGTCGCGATGCTGGGTGTCCTTGACCCCCACCGTGGCAGCGCCGCACCTCAACGCACCACTTCGGTCCTTGCGACGGCATGTGGATCTGATGGTGGGCGCCGCTACTATGTGTTCTGCCTTTTACATCGGCGACTTGTGTGGGGGTTTGTTTCTGATAGGCCAGGCCTTTACTTTCCAACCACGCCGCCACTGGACTACCCAGGATTGCAATTGCTCCATCTACTCAGGCCACATTACA"/>
+                            
+        <sequence id="seq_AF271886i_3319" spec="Sequence" taxon="AF271886i_3319" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACCGTTCCTGCATCAGCCATCCACTATCGCAACAGCTCGGGCGTCTACCACATCACCAATGACTGCCCCAATTCCAGCATAGTGTACGAGACTGACCATCACATCCTACACCTCCCAGGATGCGTGCCCTGTGTGAGGAGCGGGAACGAGTCGCGATGCTGGGTGTCCTTAACCCCCACCGTGGCAGCGCCGTACCAAAATGCACCACTTCAGTCCTTGCGACGGCATGTAGACCTGATGGTGGGCGCTGCTACCATGTGTTCTGCCCTTTATATCGGCGACTTGTGTGGGGGCTTGTTTTTGATAGGCCAGGCTTTTACTTTCCAACCACGCCGCCATTGGACTACTCAGGATTGCAATTGCTCCATCTACTCAGGCCACATCACA"/>
+                            
+        <sequence id="seq_AF271887i_3405" spec="Sequence" taxon="AF271887i_3405" totalcount="4" value="CTCTTGGCACTTCTCTCGTGCCTGACCGTCCCTGCCTCGGCCATACACTATCGCAATGCTTCGGATGTCTACCACGTCACCAATGACTGTCCGAATTCCAGCATAGTCTATGAGTCTGAAAACCACATCCTACACCTTCCGGGGTGTGTGCCCTGTGTGAGGATTGGGAACGTGTCACAATGCTGGGTGGCCCTAACCCCCACCGTGGCGGCGCCGTACCTCAATGCTCCGGTCGACTCCCTACGGAGGCACGTGGACCTGATGGTTGGCGCCGCTACTATGTGCTCAGCATTTTATGTTGGGGACCTGTGCGGGGCTGTGTTCCTGGCGGGCCAGTTGGTGACGTTTCGACCGCGACGCCACTGGACCACTCAAGATTGTAACTGTTCCATCTATGCCGGGCACATCACA"/>
+                        
+    </data>
+        
+
+
+    
+
+
+    
+
+    <map name="Uniform" >beast.math.distributions.Uniform</map>
+    
+    <map name="Exponential" >beast.math.distributions.Exponential</map>
+    
+    <map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
+    
+    <map name="Normal" >beast.math.distributions.Normal</map>
+    
+    <map name="Beta" >beast.math.distributions.Beta</map>
+    
+    <map name="Gamma" >beast.math.distributions.Gamma</map>
+    
+    <map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
+    
+    <map name="prior" >beast.math.distributions.Prior</map>
+    
+    <map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
+    
+    <map name="OneOnX" >beast.math.distributions.OneOnX</map>
+    
+    <tree spec='beast.util.ClusterTree' id='Tree.t:hcv' clusterType='upgma' taxa='@hcv'/>
+            
+    <run id="mcmc" spec="MCMC" chainLength="100000000">
+    
+        <state id="state" spec="State" storeEvery="5000">
+                    
+            <stateNode idref="Tree.t:hcv" />
+                    
+            <parameter id="kappa.s:hcv" spec="parameter.RealParameter" lower="0.0" name="stateNode">2.0</parameter>
+                    
+            <stateNode id="indicators.alltrees" spec="parameter.BooleanParameter">false</stateNode>
+                    
+            <parameter id="populationMean.alltrees" spec="parameter.RealParameter" name="stateNode">1.0</parameter>
+                    
+            <parameter id="popSizes.alltrees" spec="parameter.RealParameter" name="stateNode">1.0</parameter>
+                    
+            <parameter id="freqParameter.s:hcv" spec="parameter.RealParameter" dimension="4" lower="0.0" name="stateNode" upper="1.0">0.25</parameter>
+                
+        </state>
+            
+       <!-- 
+ <init id="RandomTree.t:hcv" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:hcv" taxa="@hcv">
+                    
+            <populationModel id="ConstantPopulation0.t:hcv" spec="ConstantPopulation">
+                            
+                <parameter id="randomPopSize.t:hcv" spec="parameter.RealParameter" name="popSize">1.0</parameter>
+                        
+            </populationModel>
+                
+        </init>
+ -->
+            
+        <distribution id="posterior" spec="util.CompoundDistribution">
+                    
+            <distribution id="prior" spec="util.CompoundDistribution">
+                            
+                <distribution id="ExtendedBayesianSkyline.t:hcv" spec="Coalescent">
+                                    
+                    <populationModel id="scaledDemo.t:hcv" spec="ScaledPopulationFunction">
+                                            
+                        <population id="demographic.alltrees" spec="CompoundPopulationFunction" type="stepwise" useIntervalsMiddle="false" populationIndicators="@indicators.alltrees" populationSizes="@popSizes.alltrees">
+                                                    
+                            <itree id="treeIntervals.t:hcv" spec="TreeIntervals" tree="@Tree.t:hcv"/>
+                                                
+                        </population>
+                                            
+                        <parameter id="RealParameter.3" spec="parameter.RealParameter" lower="0.0" name="factor" upper="0.0">1.0</parameter>
+                                        
+                    </populationModel>
+                                    
+                    <treeIntervals idref="treeIntervals.t:hcv"/>
+                                
+                </distribution>
+                            
+                <prior id="FrequenciesPrior.s:hcv" name="distribution" x="@freqParameter.s:hcv">
+                                    
+                    <Uniform id="Uniform.3" name="distr"/>
+                                
+                </prior>
+                            
+                <prior id="indicatorsPrior.alltrees" name="distribution">
+                                    
+                    <x id="indsSun.alltrees" spec="util.Sum">
+                                            
+                        <arg idref="indicators.alltrees"/>
+                                        
+                    </x>
+                                    
+                    <distr id="Poisson.EBSP" spec="beast.math.distributions.Poisson">
+                                            
+                        <parameter id="RealParameter.4" spec="parameter.RealParameter" estimate="false" name="lambda" upper="0.0">0.69314718056</parameter>
+                                        
+                    </distr>
+                                
+                </prior>
+                            
+                <prior id="KappaPrior.s:hcv" name="distribution" x="@kappa.s:hcv">
+                                    
+                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
+                                            
+                        <parameter id="RealParameter.1" spec="parameter.RealParameter" estimate="false" name="M">1.0</parameter>
+                                            
+                        <parameter id="RealParameter.2" spec="parameter.RealParameter" estimate="false" name="S">1.25</parameter>
+                                        
+                    </LogNormal>
+                                
+                </prior>
+                            
+                <prior id="popSizePrior.alltrees" name="distribution" x="@popSizes.alltrees">
+                                    
+                    <Exponential id="popPriorDist.EBSP" mean="@populationMean.alltrees" name="distr"/>
+                                
+                </prior>
+                            
+                <prior id="populationMeanPrior.alltrees" name="distribution" x="@populationMean.alltrees">
+                                    
+                    <OneOnX id="OneOnX.EBSP" name="distr"/>
+                                
+                </prior>
+                        
+            </distribution>
+                    
+            <distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
+                            
+                <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@hcv" tree="@Tree.t:hcv">
+                                    
+                    <siteModel id="SiteModel.s:hcv" spec="SiteModel">
+                                            
+                        <parameter id="mutationRate.s:hcv" spec="parameter.RealParameter" estimate="false" name="mutationRate">1.0</parameter>
+                                            
+                        <parameter id="gammaShape.s:hcv" spec="parameter.RealParameter" estimate="false" name="shape">1.0</parameter>
+                                            
+                        <parameter id="proportionInvariant.s:hcv" spec="parameter.RealParameter" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
+                                            
+                        <substModel id="hky.s:hcv" spec="HKY" kappa="@kappa.s:hcv">
+                                                    
+                            <frequencies id="estimatedFreqs.s:hcv" spec="Frequencies" frequencies="@freqParameter.s:hcv"/>
+                                                
+                        </substModel>
+                                        
+                    </siteModel>
+                                    
+                    <branchRateModel id="StrictClock.c:hcv" spec="beast.evolution.branchratemodel.StrictClockModel">
+                                            
+                        <parameter id="clockRate.c:hcv" spec="parameter.RealParameter" estimate="false" name="clock.rate">1.0</parameter>
+                                        
+                    </branchRateModel>
+                                
+                </distribution>
+                        
+            </distribution>
+                
+        </distribution>
+            
+        <operator id="KappaScaler.s:hcv" spec="ScaleOperator" parameter="@kappa.s:hcv" scaleFactor="0.5" weight="0.1"/>
+            
+        <operator id="ExtendedBayesianSkylineTreeScaler.t:hcv" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:hcv" weight="3.0"/>
+            
+        <operator id="ExtendedBayesianSkylineTreeRootScaler.t:hcv" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:hcv" weight="3.0"/>
+            
+        <operator id="ExtendedBayesianSkylineUniformOperator.t:hcv" spec="Uniform" tree="@Tree.t:hcv" weight="30.0"/>
+            
+        <operator id="ExtendedBayesianSkylineSubtreeSlide.t:hcv" spec="SubtreeSlide" tree="@Tree.t:hcv" weight="15.0"/>
+            
+        <operator id="ExtendedBayesianSkylineNarrow.t:hcv" spec="Exchange" tree="@Tree.t:hcv" weight="15.0"/>
+            
+        <operator id="ExtendedBayesianSkylineWide.t:hcv" spec="Exchange" isNarrow="false" tree="@Tree.t:hcv" weight="3.0"/>
+            
+        <operator id="ExtendedBayesianSkylineWilsonBalding.t:hcv" spec="WilsonBalding" tree="@Tree.t:hcv" weight="3.0"/>
+            
+        <operator id="bitflip.alltrees" spec="BitFlipOperator" parameter="@indicators.alltrees" weight="30.0"/>
+            
+        <operator id="indicatorSampler.alltrees" spec="SampleOffValues" dist="@popPriorDist.EBSP" indicators="@indicators.alltrees" values="@popSizes.alltrees" weight="15.0"/>
+            
+        <operator id="indicatorScaler.alltrees" spec="ScaleOperator" degreesOfFreedom="1" indicator="@indicators.alltrees" parameter="@popSizes.alltrees" scaleFactor="0.5" weight="15.0"/>
+            
+        <operator id="EBSPupDownOperator.alltrees" spec="UpDownOperator" scaleFactor="0.7" weight="5.0">
+                    
+            <up idref="popSizes.alltrees"/>
+                    
+            <up idref="populationMean.alltrees"/>
+                
+        </operator>
+            
+        <operator id="FrequenciesExchanger.s:hcv" spec="DeltaExchangeOperator" delta="0.01" weight="0.1">
+                    
+            <parameter idref="freqParameter.s:hcv"/>
+                
+        </operator>
+            
+        <logger id="tracelog" spec="Logger" fileName="test.$(seed).log" logEvery="25000" model="@posterior" sanitiseHeaders="true" sort="smart">
+                    
+            <log idref="posterior"/>
+            <log idref="likelihood"/>                    
+            <log idref="prior"/>
+                    
+            <log idref="treeLikelihood"/>
+            <log id="treeStats" spec='beast.evolution.tree.TreeStatLogger' tree='@Tree.t:hcv' logLength="true"/>        
+
+            <log idref="ExtendedBayesianSkyline.t:hcv"/>            
+            <log id="sumIndicators" spec="util.Sum">
+                <arg idref="indicators.alltrees"/>
+            </log>
+            <log idref="populationMean.alltrees"/>
+            <log idref="popSizes.alltrees"/>
+            <log idref="indicators.alltrees"/>
+                  
+            <log idref="kappa.s:hcv"/>
+            <log idref="freqParameter.s:hcv"/>
+                
+        </logger>
+            
+        <logger id="screenlog" spec="Logger" logEvery="5000000">
+                    
+            <log idref="posterior"/>
+                    
+            <log idref="likelihood"/>
+                    
+            <log idref="prior"/>
+            
+            <log idref="treeStats" />
+                
+        </logger>
+            
+        <logger id="treelog.t:hcv" spec="Logger" fileName="$(tree).trees" logEvery="25000" mode="tree">
+                    
+            <log id="TreeWithMetaDataLogger.t:hcv" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:hcv"/>
+                
+        </logger>
+            
+        <logger id="EBSPLogger" spec="Logger" fileName="EBSP.log" logEvery="25000" model="@demographic.alltrees">
+                    
+            <log idref="demographic.alltrees"/>
+                
+        </logger>
+            
+        <operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
+        
+
+    </run>
+    
+</beast>
diff -Nru beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/testEBSP-old.xml beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/testEBSP-old.xml
--- beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/testEBSP-old.xml	1970-01-01 00:00:00.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/testEBSP-old.xml	2022-04-04 07:18:36.000000000 +0000
@@ -0,0 +1,322 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<beast namespace="beast.core:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.core.parameter:beast.math.distributions"
+       version="2.0">
+
+
+    <data dataType="nucleotide" id="alignment.26" name="taxa">
+        <sequence id="seq_Orthogeomys_heterodus" taxon="Orthogeomys_heterodus" totalcount="4"
+                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGAGGTATTACAATACCAGACTTCAAACTTTACTATAGAGCCATAATAACAAAAACCGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAATGGAAYAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGTCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCACCATGCACAGGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCAGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGGGAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATAGGAGAAAGACTCAATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAATAATACATCTGACAAATGCTTGAT--ATCCAGT-ATCTACAGGGAACTCAAGAAATTAATC"/>
+        <sequence id="seq_Thomomys_bottae_awahnee_a" taxon="Thomomys_bottae_awahnee_a" totalcount="4"
+                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACMCAGTCTATTCAATTATTGGKGCTGGCAAAACTGGGCAGCCMCATGCARAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_awahnee_b" taxon="Thomomys_bottae_awahnee_b" totalcount="4"
+                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCM-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGT????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_xerophilus" taxon="Thomomys_bottae_xerophilus" totalcount="4"
+                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAAYTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_cactophilus" taxon="Thomomys_bottae_cactophilus" totalcount="4"
+                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAAYTGTTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAA????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_albatus" taxon="Thomomys_bottae_albatus" totalcount="4"
+                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGATCCAGAAATAGAACCAC-ATACCTATAGTCAACTTGTATTTGATAAAGGAGCTAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCATTTCACCATGCACAAGAATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCT-------------------------------------CATAGGCACTCATAGGCACAGGCAAAAGATTCCTATACAGGAACCCAGGGTCAACAACAGATTGGAGAGAGACTCAATAAATGGGACTACCTAAAAATAAAA-GTTTCTGCAC?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_ruidosae" taxon="Thomomys_bottae_ruidosae" totalcount="4"
+                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCARAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAAYTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAG??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_bottae" taxon="Thomomys_bottae_bottae" totalcount="4"
+                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAAATTCCTGAACAGAATCCCAGGGTCA-CAACAGATKGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATA?????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_alpinus" taxon="Thomomys_bottae_alpinus" totalcount="4"
+                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCTATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCA??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_riparius" taxon="Thomomys_bottae_riparius" totalcount="4"
+                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACA???????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_mewa" taxon="Thomomys_bottae_mewa" totalcount="4"
+                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCATTTCACCATGCACAAGAATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAA???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_saxatilis" taxon="Thomomys_bottae_saxatilis" totalcount="4"
+                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_bottae_laticeps" taxon="Thomomys_bottae_laticeps" totalcount="4"
+                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAATTGCTACATGATAAWGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCAATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATAT????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_talpoides_ocius" taxon="Thomomys_talpoides_ocius" totalcount="4"
+                  value="???CTAGGCAAAA-G-AGC-ATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CKCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
+        <sequence id="seq_Thomomys_idahoensis_pygmaeus_a" taxon="Thomomys_idahoensis_pygmaeus_a" totalcount="4"
+                  value="????????CAAAA-G-AGCAATGCTGGTGGTATYACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
+        <sequence id="seq_Thomomys_idahoensis_pygmaeus_b" taxon="Thomomys_idahoensis_pygmaeus_b" totalcount="4"
+                  value="????GGCGCAAAA-G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGCTATCTACAGAGAACTCAAGAAACTAATC"/>
+        <sequence id="seq_Thomomys_mazama_mazama" taxon="Thomomys_mazama_mazama" totalcount="4"
+                  value="ATTCTAGGCAAAAAGAAGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
+        <sequence id="seq_Thomomys_mazama_nasicus" taxon="Thomomys_mazama_nasicus" totalcount="4"
+                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCSCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTA-TC"/>
+        <sequence id="seq_Thomomys_monticola_a" taxon="Thomomys_monticola_a" totalcount="4"
+                  value="??????????????G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGYCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
+        <sequence id="seq_Thomomys_monticola_b" taxon="Thomomys_monticola_b" totalcount="4"
+                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATYACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAWATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAATGGAACRAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATATATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
+        <sequence id="seq_Thomomys_talpoides_yakimensis" taxon="Thomomys_talpoides_yakimensis" totalcount="4"
+                  value="ATTCTAGGCAAAA-G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTKTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
+        <sequence id="seq_Thomomys_talpoides_bridgeri" taxon="Thomomys_talpoides_bridgeri" totalcount="4"
+                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATCCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
+        <sequence id="seq_Thomomys_townsendii_townsendii" taxon="Thomomys_townsendii_townsendii" totalcount="4"
+                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTYGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTCTGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCCACAATACATCTGACAAATGCTTAAT--ATCCAGT-ATCTACAGG-AACTCAAG?????????"/>
+        <sequence id="seq_Thomomys_townsendii_relictus" taxon="Thomomys_townsendii_relictus" totalcount="4"
+                  value="??????????????G-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTAYTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCACTATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAATGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAATTGCTACATGATAAWGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAATGTTTCTGTACAGATAAAAACATAG???????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_umbrinus_chihuahuae" taxon="Thomomys_umbrinus_chihuahuae" totalcount="4"
+                  value="?????????????AG-AGC-ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCTTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATACATCTGACAAATGCTTAAT--ATCCAGT-ATCTACA????????????????????"/>
+        <sequence id="seq_Thomomys_umbrinus_atroavarius" taxon="Thomomys_umbrinus_atroavarius" totalcount="4"
+                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGCATTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGKCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGYCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAATTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCCACAATACATCTGACAAATGCTT-ATATATCCAGT-ATCTACAGAGAACTCAAG?????????"/>
+    </data>
+    <data dataType="nucleotide" id="alignment.29" name="taxa">
+        <sequence id="seq_Orthogeomys_heterodus1" taxon="Orthogeomys_heterodus" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCACAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCGTTTCTGGAAAACTGAGATCTTGTTTTGACCAACAGAAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGATGTCTCTGTCAGGATCTAGTCCCATCCTG-AATCCATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTCAGAACTGACTGAATCAGGCCAGTGAAAGTTA-CAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATTGTGCATGGCTTCATTAGCAGGTTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCATCAGATTGTCAGGGTCTTGGATTCTGATAAGTTCTGTGTTCCTGATGAGAGACTGGTTATTCAGTAAGTTGTAGGACAAA"/>
+        <sequence id="seq_Thomomys_bottae_awahnee_a1" taxon="Thomomys_bottae_awahnee_a" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGAGAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_awahnee_b1" taxon="Thomomys_bottae_awahnee_b" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGAKAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_xerophilus1" taxon="Thomomys_bottae_xerophilus" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCACTAAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTRTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_cactophilus1" taxon="Thomomys_bottae_cactophilus" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTACCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCACTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCASTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_albatus1" taxon="Thomomys_bottae_albatus" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGTGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_ruidosae1" taxon="Thomomys_bottae_ruidosae" totalcount="4"
+                  value="?????????????????????????????C-AGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_bottae1" taxon="Thomomys_bottae_bottae" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACYGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTAKGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCRTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_alpinus1" taxon="Thomomys_bottae_alpinus" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCC-AGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGTTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCYACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_riparius1" taxon="Thomomys_bottae_riparius" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_mewa1" taxon="Thomomys_bottae_mewa" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAATTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_saxatilis1" taxon="Thomomys_bottae_saxatilis" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_bottae_laticeps1" taxon="Thomomys_bottae_laticeps" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_talpoides_ocius1" taxon="Thomomys_talpoides_ocius" totalcount="4"
+                  value="C-AGCTTGCTGGTCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCATATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAAWGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGACAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_idahoensis_pygmaeus_a1" taxon="Thomomys_idahoensis_pygmaeus_a" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTTTAAGTGTTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGTCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGTCCAGTGAAACTTAACAGCTACCTTGCCAATKGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGG--TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCGGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_idahoensis_pygmaeus_b1" taxon="Thomomys_idahoensis_pygmaeus_b" totalcount="4"
+                  value="CAAGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTGTTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGTCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGG--TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCGGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_mazama_mazama1" taxon="Thomomys_mazama_mazama" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTATTGCCTGGATATAGTGTCTATAGACAGAGACAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCACATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCACCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAG-CGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_mazama_nasicus1" taxon="Thomomys_mazama_nasicus" totalcount="4"
+                  value="C-AGCTTGCTG-TCACAATGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTATTGCCTGGATATAGTGTCTATAGACAGAGACAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCACATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAG-CGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_monticola_a1" taxon="Thomomys_monticola_a" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGACGCCKTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAGGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_monticola_b1" taxon="Thomomys_monticola_b" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGACGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTYCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAGGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_talpoides_yakimensis1" taxon="Thomomys_talpoides_yakimensis" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGAMTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_talpoides_bridgeri1" taxon="Thomomys_talpoides_bridgeri" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_townsendii_townsendii1" taxon="Thomomys_townsendii_townsendii" totalcount="4"
+                  value="C-AGCTTGCTGGTCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_townsendii_relictus1" taxon="Thomomys_townsendii_relictus" totalcount="4"
+                  value="C-AGCTTGCTGGTCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_umbrinus_chihuahuae1" taxon="Thomomys_umbrinus_chihuahuae" totalcount="4"
+                  value="C-AGCTTGCTGGTCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAAGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTGGAATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGAGGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+        <sequence id="seq_Thomomys_umbrinus_atroavarius1" taxon="Thomomys_umbrinus_atroavarius" totalcount="4"
+                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
+    </data>
+    <data dataType="nucleotide" id="alignment.47" name="taxa">
+        <sequence id="seq_Orthogeomys_heterodus2" taxon="Orthogeomys_heterodus" totalcount="4"
+                  value="CATGATTTTGTCATGCCTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGATGATTGACGCTGCTGTCAGTAGTGAGTGACACAAATTTTATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACGTGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAATTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATTTCTTTTCCA-CC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGATTTTATGGGACTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTAYCTGAAGGTTATTGATGGTGACCTCATTTTCTTGTGCTTGTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAATTCAGAGTTTGAACACTGTCCTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTCTATGTATGTGGTACCGTGCACTCAAACCCAGGTCTTTGTGAATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGCAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_awahnee_a2" taxon="Thomomys_bottae_awahnee_a" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACARAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGACGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_awahnee_b2" taxon="Thomomys_bottae_awahnee_b" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAMGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_xerophilus2" taxon="Thomomys_bottae_xerophilus" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_cactophilus2" taxon="Thomomys_bottae_cactophilus" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_albatus2" taxon="Thomomys_bottae_albatus" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_ruidosae2" taxon="Thomomys_bottae_ruidosae" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTYGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_bottae2" taxon="Thomomys_bottae_bottae" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTYGTTTTCACCTGTGTGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCYGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGGTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAYGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_alpinus2" taxon="Thomomys_bottae_alpinus" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCYGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAYGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_riparius2" taxon="Thomomys_bottae_riparius" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_mewa2" taxon="Thomomys_bottae_mewa" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_saxatilis2" taxon="Thomomys_bottae_saxatilis" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTARGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_bottae_laticeps2" taxon="Thomomys_bottae_laticeps" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_talpoides_ocius2" taxon="Thomomys_talpoides_ocius" totalcount="4"
+                  value="CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTATTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTT--------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTC-TATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATCTCTTTGTCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTGTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGTA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A"/>
+        <sequence id="seq_Thomomys_idahoensis_pygmaeus_a2" taxon="Thomomys_idahoensis_pygmaeus_a" totalcount="4"
+                  value="???????TTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTCGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------T--GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGACTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTA--------CCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTA?????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_idahoensis_pygmaeus_b2" taxon="Thomomys_idahoensis_pygmaeus_b" totalcount="4"
+                  value="?ATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACTAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTATACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATGTTTTTTTT-G------------------------------CACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCACCACTTCTGGCTTTTTTTTTTCTACGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGCTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATTATGTTTGTGCAA????"/>
+        <sequence id="seq_Thomomys_mazama_mazama2" taxon="Thomomys_mazama_mazama" totalcount="4"
+                  value="??????????????????????A---GCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------------------------------------------------------------------------------TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAAGCACTTTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGTTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTT?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_mazama_nasicus2" taxon="Thomomys_mazama_nasicus" totalcount="4"
+                  value="??????????????GCTTTCTTACGTGCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCTTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAGGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTGTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTCC---------GGTACCATGCACTGGAACCCAGGTCTTCGTGCATGCTGGACAGCAACTCTACCACTAGGCAAAGCTTCTGGACCCATTAGT?????????????????????????????"/>
+        <sequence id="seq_Thomomys_monticola_a2" taxon="Thomomys_monticola_a" totalcount="4"
+                  value="CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGATCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A"/>
+        <sequence id="seq_Thomomys_monticola_b2" taxon="Thomomys_monticola_b" totalcount="4"
+                  value="CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAAYGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTT--GCCAGTCCTGGGCTTSAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTKTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGAYCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCYAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A"/>
+        <sequence id="seq_Thomomys_talpoides_yakimensis2" taxon="Thomomys_talpoides_yakimensis" totalcount="4"
+                  value="?????????????????TTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGCTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAGTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------TTTGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCAGTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGTCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAATACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCAC???????????????????????????????????????????????????????"/>
+        <sequence id="seq_Thomomys_talpoides_bridgeri2" taxon="Thomomys_talpoides_bridgeri" totalcount="4"
+                  value="CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTCGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCYCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A"/>
+        <sequence id="seq_Thomomys_townsendii_townsendii2" taxon="Thomomys_townsendii_townsendii" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACACAAATTTCATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCCTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTT--ATATCATCTTTGTGCAACT-A"/>
+        <sequence id="seq_Thomomys_townsendii_relictus2" taxon="Thomomys_townsendii_relictus" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_umbrinus_chihuahuae2" taxon="Thomomys_umbrinus_chihuahuae" totalcount="4"
+                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTRCCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
+        <sequence id="seq_Thomomys_umbrinus_atroavarius2" taxon="Thomomys_umbrinus_atroavarius" totalcount="4"
+                  value="CATGATTTTGTCATGYTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTYGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTTYATATCATCTTTGTGAAACT-A"/>
+    </data>
+
+    <plate spec='Plate' var='n' range='.26,.29,.47'>
+        <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
+        <input spec='HKY' id='hky$(n)' kappa='@hky.kappa$(n)'>
+            <frequencies spec='Frequencies' frequencies='@hky.frequencies$(n)'/>
+        </input>
+
+        <!-- site model                                                              -->
+        <input spec='SiteModel' id="siteModel$(n)" substModel='@hky$(n)'/>
+
+        <tree spec='beast.util.ClusterTree' id='tree$(n)' clusterType='upgma' taxa='@alignment$(n)'/>
+
+        <input spec='TreeLikelihood' id="treeLikelihood$(n)"
+               data="@alignment$(n)"
+               tree="@tree$(n)"
+               siteModel="@siteModel$(n)"/>
+
+        <parameter id="hky.kappa$(n)" value="2.0" lower="0.0"/>
+        <parameter id="hky.frequencies$(n)" value="0.25" dimension="4"/>
+    </plate>
+
+    <parameter id="popSizes" value="0.017" lower="0.0"/>
+    <input name="indicators" spec='BooleanParameter' id='indicators' value="false"/>
+    <parameter id="populationMean" value="0.017" lower="0.0"/>
+
+    <run spec="MCMC" id="mcmc" chainLength="20000000"> <!--autoOptimize="true"-->
+        <state>
+            <plate spec='Plate' var='n' range='.26,.29,.47'>
+                <stateNode idref='hky.kappa$(n)'/>
+                <stateNode idref='hky.frequencies$(n)'/>
+                <stateNode idref='tree$(n)'/>
+            </plate>
+            <stateNode idref='popSizes'/>
+            <stateNode idref='indicators'/>
+            <stateNode idref='populationMean'/>
+        </state>
+
+        <distribution id="posterior" spec="CompoundDistribution">
+            <distribution id="prior" spec="CompoundDistribution">
+                <distribution spec="Prior" x="@populationMean">
+                    <distr offset="0.0" spec="OneOnX"/>
+                </distribution>
+                <distribution spec="Prior">
+                    <x arg="@indicators" id="indsSun" spec="Sum"/>
+                    <distr offset="0.0" spec="Poisson">
+                        <parameter dimension="1" estimate="true" lower="0.0" name="lambda" upper="0.0" value="0.6931471805599453"/>
+                    </distr>
+                </distribution>
+                <distribution id="populationMeanPrior" spec="Prior" x="@popSizes">
+                    <distr id="popPriorDist" mean="@populationMean" offset="0.0" spec="Exponential"/>
+                </distribution>
+
+                <distribution id="coalescent" spec="CompoundDistribution">
+                    <distribution id="Coal.26" spec="Coalescent" treeIntervals="@TreeIntervals.26">
+                        <populationModel id="scaledDemo4" spec="beast.evolution.tree.coalescent.ScaledPopulationFunction">
+                            <population id="demographic" populationIndicators="@indicators" populationSizes="@popSizes"
+                                        spec="beast.evolution.tree.coalescent.CompoundPopulationFunction" type="linear"
+                                        useIntervalsMiddle="false">
+                                <plate spec='Plate' var='n' range='.26,.29,.47'>
+                                    <itree id="TreeIntervals$(n)" spec="TreeIntervals" tree="@tree$(n)"/>
+                                </plate>
+                            </population>
+                            <parameter dimension="1" estimate="true" lower="0.0" name="factor" upper="0.0" value="3"/>
+                        </populationModel>
+                    </distribution>
+
+                    <distribution id="Coal.29" populationModel="@scaledDemo4" spec="Coalescent" treeIntervals="@TreeIntervals.29"/>
+                    <distribution id="Coal.47" populationModel="@scaledDemo4" spec="Coalescent" treeIntervals="@TreeIntervals.47"/>
+                </distribution>
+
+                <plate spec='Plate' var='n' range='.26,.29,.47'>
+                    <distribution spec="Prior" x="@hky.kappa$(n)">
+                        <distr M="1.0" S="1.25" meanInRealSpace="false" spec="LogNormalDistributionModel"/>
+                    </distribution>
+                    <distribution spec="Prior" x="@hky.frequencies$(n)">
+                        <distr lower="0.0" upper="1.0" spec="beast.math.distributions.Uniform"/>
+                    </distribution>
+                </plate>
+            </distribution>
+
+            <distribution id="likelihood" spec="CompoundDistribution">
+                <plate spec='Plate' var='n' range='.26,.29,.47'>
+                    <distribution idref="treeLikelihood$(n)"/>
+                </plate>
+            </distribution>
+        </distribution>
+
+
+        <operator id="bitflip" parameter="@indicators" spec="BitFlipOperator" uniform="true" weight="30.0"/>
+        <operator dist="@popPriorDist" indicators="@indicators" spec="beast.evolution.tree.coalescent.SampleOffValues"
+                  values="@popSizes" weight="15.0"/>
+        <operator degreesOfFreedom="1" indicator="@indicators" parameter="@popSizes" scaleAll="false"
+                  scaleAllIndependently="false" scaleFactor="0.5" spec="ScaleOperator" weight="6.0"/>
+        <operator spec='ScaleOperator' scaleFactor="0.9" weight="3" parameter="@populationMean"/>
+        <operator scaleFactor="0.7" spec="UpDownOperator" weight="30.0">
+            <down idref="popSizes"/>
+            <down idref="populationMean"/>
+            <plate spec='Plate' var='n' range='.26,.29,.47'>
+                <down idref="tree$(n)"/>
+            </plate>
+        </operator>
+
+        <plate spec='Plate' var='n' range='.26,.29,.47'>
+            <operator spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa$(n)"/>
+            <operator spec='DeltaExchangeOperator' delta="0.01" weight="0.1" parameter="@hky.frequencies$(n)"/>
+            <operator spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree$(n)"/>
+            <operator spec='Uniform' weight="30" tree="@tree$(n)"/>
+            <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree$(n)"/>
+            <operator spec='Exchange' isNarrow='true' weight="15" tree="@tree$(n)"/>
+            <operator spec='Exchange' isNarrow='false' weight="3" tree="@tree$(n)"/>
+            <operator spec='WilsonBalding' weight="1" tree="@tree$(n)"/>
+            <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree$(n)"/>
+        </plate>
+
+        <logger logEvery="1000000" mode="autodetect">
+            <log idref="posterior"/>
+            <log idref="prior"/>
+            <log idref="likelihood"/>
+            <log idref="populationMean"/>
+            <log spec="Sum" arg="@indicators"/>
+            <log idref="indicators"/>
+            <plate spec='Plate' var='n' range='.26,.29,.47'>
+                <log spec='beast.evolution.tree.TreeHeightLogger' tree='@tree$(n)'/>
+                <log idref="hky.kappa$(n)"/>
+                <log idref="hky.frequencies$(n)"/>
+                <log idref="treeLikelihood$(n)"/>
+            </plate>
+            <log idref="coalescent"/>
+            <log idref="popSizes"/>
+        </logger>
+
+        <logger fileName="test.$(seed).log" logEvery="5000" mode="autodetect" model="@posterior">
+            <log idref="posterior"/>
+            <log idref="prior"/>
+            <log idref="likelihood"/>
+            <plate spec='Plate' var='n' range='.26,.29,.47'>
+                <log spec='beast.evolution.tree.TreeStatLogger' tree='@tree$(n)' logLength="false"/>
+            </plate>
+            <log spec="Sum" arg="@indicators"/>
+            <log idref="populationMean"/>
+            <log idref="popSizes"/>
+            <log idref="indicators"/>
+            <plate spec='Plate' var='n' range='.26,.29,.47'>
+                <log idref="hky.kappa$(n)"/>
+                <log idref="hky.frequencies$(n)"/>
+            </plate>
+            <plate spec='Plate' var='n' range='.26,.29,.47'>
+                <log idref="treeLikelihood$(n)"/>
+            </plate>
+            <log idref="coalescent"/>
+
+        </logger>
+    </run>
+
+</beast>
diff -Nru beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/testEBSP.xml beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/testEBSP.xml
--- beast2-mcmc-2.6.6+dfsg/examples/beast2vs1/testEBSP.xml	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/examples/beast2vs1/testEBSP.xml	1970-01-01 00:00:00.000000000 +0000
@@ -1,317 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast namespace="beast.core:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.core.parameter:beast.math.distributions"
-       version="2.0">
-
-
-    <data dataType="nucleotide" id="alignment.26" name="taxa">
-        <sequence id="seq_Orthogeomys_heterodus" taxon="Orthogeomys_heterodus" totalcount="4"
-                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGAGGTATTACAATACCAGACTTCAAACTTTACTATAGAGCCATAATAACAAAAACCGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAATGGAAYAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGTCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCACCATGCACAGGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCAGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGGGAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATAGGAGAAAGACTCAATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAATAATACATCTGACAAATGCTTGAT--ATCCAGT-ATCTACAGGGAACTCAAGAAATTAATC"/>
-        <sequence id="seq_Thomomys_bottae_awahnee_a" taxon="Thomomys_bottae_awahnee_a" totalcount="4"
-                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACMCAGTCTATTCAATTATTGGKGCTGGCAAAACTGGGCAGCCMCATGCARAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_awahnee_b" taxon="Thomomys_bottae_awahnee_b" totalcount="4"
-                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCM-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGT????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_xerophilus" taxon="Thomomys_bottae_xerophilus" totalcount="4"
-                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAAYTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_cactophilus" taxon="Thomomys_bottae_cactophilus" totalcount="4"
-                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAAYTGTTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAA????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_albatus" taxon="Thomomys_bottae_albatus" totalcount="4"
-                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGATCCAGAAATAGAACCAC-ATACCTATAGTCAACTTGTATTTGATAAAGGAGCTAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCATTTCACCATGCACAAGAATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCT-------------------------------------CATAGGCACTCATAGGCACAGGCAAAAGATTCCTATACAGGAACCCAGGGTCAACAACAGATTGGAGAGAGACTCAATAAATGGGACTACCTAAAAATAAAA-GTTTCTGCAC?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_ruidosae" taxon="Thomomys_bottae_ruidosae" totalcount="4"
-                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCARAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAAYTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAG??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_bottae" taxon="Thomomys_bottae_bottae" totalcount="4"
-                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAAATTCCTGAACAGAATCCCAGGGTCA-CAACAGATKGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATA?????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_alpinus" taxon="Thomomys_bottae_alpinus" totalcount="4"
-                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCTATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCA??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_riparius" taxon="Thomomys_bottae_riparius" totalcount="4"
-                  value="????????????????AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACA???????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_mewa" taxon="Thomomys_bottae_mewa" totalcount="4"
-                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCATTTCACCATGCACAAGAATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAA???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_saxatilis" taxon="Thomomys_bottae_saxatilis" totalcount="4"
-                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_bottae_laticeps" taxon="Thomomys_bottae_laticeps" totalcount="4"
-                  value="????????????????????ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAATTGCTACATGATAAWGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCAATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTT-GCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATAT????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_talpoides_ocius" taxon="Thomomys_talpoides_ocius" totalcount="4"
-                  value="???CTAGGCAAAA-G-AGC-ATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CKCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
-        <sequence id="seq_Thomomys_idahoensis_pygmaeus_a" taxon="Thomomys_idahoensis_pygmaeus_a" totalcount="4"
-                  value="????????CAAAA-G-AGCAATGCTGGTGGTATYACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
-        <sequence id="seq_Thomomys_idahoensis_pygmaeus_b" taxon="Thomomys_idahoensis_pygmaeus_b" totalcount="4"
-                  value="????GGCGCAAAA-G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATMCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGCTATCTACAGAGAACTCAAGAAACTAATC"/>
-        <sequence id="seq_Thomomys_mazama_mazama" taxon="Thomomys_mazama_mazama" totalcount="4"
-                  value="ATTCTAGGCAAAAAGAAGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
-        <sequence id="seq_Thomomys_mazama_nasicus" taxon="Thomomys_mazama_nasicus" totalcount="4"
-                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCSCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTA-TC"/>
-        <sequence id="seq_Thomomys_monticola_a" taxon="Thomomys_monticola_a" totalcount="4"
-                  value="??????????????G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGYCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATRTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
-        <sequence id="seq_Thomomys_monticola_b" taxon="Thomomys_monticola_b" totalcount="4"
-                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATYACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAWATAGAACCAC-ACAACTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAATGGAACRAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATATATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
-        <sequence id="seq_Thomomys_talpoides_yakimensis" taxon="Thomomys_talpoides_yakimensis" totalcount="4"
-                  value="ATTCTAGGCAAAA-G-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTKTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATACAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAAYTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
-        <sequence id="seq_Thomomys_talpoides_bridgeri" taxon="Thomomys_talpoides_bridgeri" totalcount="4"
-                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATCACAATACCAGACTTCAAACTTTACTATAAAGCCATAATAACAAAAACTGC-TTGGTACTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGATATAGAACCAC-ACAACTATAGGCAACTTRTATTTGACAAAGGAGCCAAAGATATCCAATGGAACGAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGAAAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCRACGTCAGACCGGAAACCGTGAAACTGCTACATGATAATGTAGGAGAGACACTGGAACTCATAGGCACAGGAAACAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGACAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGACAAAAACATAGT-CGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATGTATCTGACAAATGCTTAAT--ATCCAGC-ATCTACAGAGAACTCAAGAAACTAATC"/>
-        <sequence id="seq_Thomomys_townsendii_townsendii" taxon="Thomomys_townsendii_townsendii" totalcount="4"
-                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTYGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGTCTGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCCACAATACATCTGACAAATGCTTAAT--ATCCAGT-ATCTACAGG-AACTCAAG?????????"/>
-        <sequence id="seq_Thomomys_townsendii_relictus" taxon="Thomomys_townsendii_relictus" totalcount="4"
-                  value="??????????????G-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTAYTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCACTATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACAATGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAACGTCAGACCGGAAACCGTGAAATTGCTACATGATAAWGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAATGTTTCTGTACAGATAAAAACATAG???????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_umbrinus_chihuahuae" taxon="Thomomys_umbrinus_chihuahuae" totalcount="4"
-                  value="?????????????AG-AGC-ATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGC-TTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGGCAACTTGTATTTGACAAAGGAGCCAAAGATATACARTGGAACAAACACAGTCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCTTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAATGTCAGACCGGAAACCGTGAAACTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCAACAATACATCTGACAAATGCTTAAT--ATCCAGT-ATCTACA????????????????????"/>
-        <sequence id="seq_Thomomys_umbrinus_atroavarius" taxon="Thomomys_umbrinus_atroavarius" totalcount="4"
-                  value="ATTCTAGGCAAAAAG-AGCAATGCTGGTGGTATTACAATACCAGACTTCAAACTCTACTATAGAGCCATAATAACAAAAACTGCATTGGTATTGGCACAAAAACAGACCAGAAGATCAGTGGAACAGAATAGAAGACCCAGAAATAGAACCAC-ATACCTATAGKCAACTTGTATTTGACAAAGGAGCCAAAGATATACAGTGGAACAAACACAGYCTATTCAATTATTGGTGCTGGCAAAACTGGGCAGCCACATGCAGAAAACTAAAAATTGACCCTAGCCTTTCGCCATGCACAAGCATTAACTCAAAGTGGATCAAAGACCTCAAYGTCAGACCGGAAACCGTGAAATTGCTACATGATAAAGTAGGAGAGACACTGGAACTCATAGGCACAGGCAAAAGATTCCTGAACAGAATCCCAGGGTCA-CAACAGATTGGAGAGAGACTCGATAAATGGGACTACCTAAAAATAAAAAGTTTCTGTACAGATAAAAACATAGT-TGCAAAAGTAGAGAGACAGCCAACCAACTGGGAAAAGATATTCACCCACAATACATCTGACAAATGCTT-ATATATCCAGT-ATCTACAGAGAACTCAAG?????????"/>
-    </data>
-    <data dataType="nucleotide" id="alignment.29" name="taxa">
-        <sequence id="seq_Orthogeomys_heterodus1" taxon="Orthogeomys_heterodus" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCACAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCGTTTCTGGAAAACTGAGATCTTGTTTTGACCAACAGAAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGATGTCTCTGTCAGGATCTAGTCCCATCCTG-AATCCATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTCAGAACTGACTGAATCAGGCCAGTGAAAGTTA-CAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATTGTGCATGGCTTCATTAGCAGGTTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCATCAGATTGTCAGGGTCTTGGATTCTGATAAGTTCTGTGTTCCTGATGAGAGACTGGTTATTCAGTAAGTTGTAGGACAAA"/>
-        <sequence id="seq_Thomomys_bottae_awahnee_a1" taxon="Thomomys_bottae_awahnee_a" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGAGAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_awahnee_b1" taxon="Thomomys_bottae_awahnee_b" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGAKAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_xerophilus1" taxon="Thomomys_bottae_xerophilus" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCACTAAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTRTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_cactophilus1" taxon="Thomomys_bottae_cactophilus" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTACCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCACTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCASTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_albatus1" taxon="Thomomys_bottae_albatus" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGTGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_ruidosae1" taxon="Thomomys_bottae_ruidosae" totalcount="4"
-                  value="?????????????????????????????C-AGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_bottae1" taxon="Thomomys_bottae_bottae" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACYGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTAKGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCRTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_alpinus1" taxon="Thomomys_bottae_alpinus" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCC-AGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGTTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCYACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_riparius1" taxon="Thomomys_bottae_riparius" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_mewa1" taxon="Thomomys_bottae_mewa" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAATTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_saxatilis1" taxon="Thomomys_bottae_saxatilis" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_bottae_laticeps1" taxon="Thomomys_bottae_laticeps" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_talpoides_ocius1" taxon="Thomomys_talpoides_ocius" totalcount="4"
-                  value="C-AGCTTGCTGGTCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCATATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAAWGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGACAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_idahoensis_pygmaeus_a1" taxon="Thomomys_idahoensis_pygmaeus_a" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTTTAAGTGTTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGTCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGTCCAGTGAAACTTAACAGCTACCTTGCCAATKGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGG--TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCGGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_idahoensis_pygmaeus_b1" taxon="Thomomys_idahoensis_pygmaeus_b" totalcount="4"
-                  value="CAAGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTGTTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGTCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGG--TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCGGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_mazama_mazama1" taxon="Thomomys_mazama_mazama" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTATTGCCTGGATATAGTGTCTATAGACAGAGACAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCACATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCACCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAG-CGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_mazama_nasicus1" taxon="Thomomys_mazama_nasicus" totalcount="4"
-                  value="C-AGCTTGCTG-TCACAATGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTATTGCCTGGATATAGTGTCTATAGACAGAGACAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCACATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCTGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCTCTGGGTTGTTAG-CGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_monticola_a1" taxon="Thomomys_monticola_a" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGACGCCKTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAGGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_monticola_b1" taxon="Thomomys_monticola_b" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGACGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTYCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAGGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_talpoides_yakimensis1" taxon="Thomomys_talpoides_yakimensis" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGTCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTGCTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGAMTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_talpoides_bridgeri1" taxon="Thomomys_talpoides_bridgeri" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTGCCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCTCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGGATCCAGTCCCATCCTG-AATTGATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGACTCTTAAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGG-TCTTTCCAAGGATTGTGCTTCTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTACTGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTGGACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_townsendii_townsendii1" taxon="Thomomys_townsendii_townsendii" totalcount="4"
-                  value="C-AGCTTGCTGGTCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_townsendii_relictus1" taxon="Thomomys_townsendii_relictus" totalcount="4"
-                  value="C-AGCTTGCTGGTCACACCGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_umbrinus_chihuahuae1" taxon="Thomomys_umbrinus_chihuahuae" totalcount="4"
-                  value="C-AGCTTGCTGGTCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAAGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTGGAATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGAGGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-        <sequence id="seq_Thomomys_umbrinus_atroavarius1" taxon="Thomomys_umbrinus_atroavarius" totalcount="4"
-                  value="C-AGCTTGCTG-TCACACTGCCCCTTCTACAAGCCCAGCTGACAGAGGCCTTAAGTACTACCTGGATATAATGTCTATAGACAGAGGCAATTCTGGAAAACTCAGATCTTATTTTGACCAACAGGAATTAATGTCTATGGTAGAATTCCCCTCAGCTCCTGGATTGCTGGTACTGGTGACGTCTCTGTCAGAATCCAGTCCCATCCTG-AATTTATACTTAACAATTTTCTAAGTATTTTGTGGTCTTGCTCTACCTCCAGGGAAGCTGGCCTGGCTATGAAAGGAAGGGCTCTTTAGAACTGACTGAATCAGGCCAGTGAAACTTAACAGCTACCTTGCCAATGGTCTGTGTGCCAGTGACATCGTGCATGGCTTCATTAGCAGATTTACTGTGCCGGGGTCTTTCCAAGGATTGTGCTTGTTGATTTGGTCCCTGGATAAATTTGCAAATGCTAATCTAGTTGTTAATGGAGAGCATCCAAACCTAAGACAGGACTATTCCTCCCTGGGTTGTTAGGCGTCAGATTGGCAGGGTCTTG-ACTCTGATAAGTTCTGTGTTCCTGATGAGAGGCTGGTTATTCAGTAAGTTGTAGGGCAAA"/>
-    </data>
-    <data dataType="nucleotide" id="alignment.47" name="taxa">
-        <sequence id="seq_Orthogeomys_heterodus2" taxon="Orthogeomys_heterodus" totalcount="4"
-                  value="CATGATTTTGTCATGCCTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGATGATTGACGCTGCTGTCAGTAGTGAGTGACACAAATTTTATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACGTGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAATTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATTTCTTTTCCA-CC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGATTTTATGGGACTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTAYCTGAAGGTTATTGATGGTGACCTCATTTTCTTGTGCTTGTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAATTCAGAGTTTGAACACTGTCCTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTCTATGTATGTGGTACCGTGCACTCAAACCCAGGTCTTTGTGAATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGCAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_awahnee_a2" taxon="Thomomys_bottae_awahnee_a" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACARAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGACGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_awahnee_b2" taxon="Thomomys_bottae_awahnee_b" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAMGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_xerophilus2" taxon="Thomomys_bottae_xerophilus" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_cactophilus2" taxon="Thomomys_bottae_cactophilus" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_albatus2" taxon="Thomomys_bottae_albatus" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_ruidosae2" taxon="Thomomys_bottae_ruidosae" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTYGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_bottae2" taxon="Thomomys_bottae_bottae" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTYGTTTTCACCTGTGTGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCYGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGGTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAYGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_alpinus2" taxon="Thomomys_bottae_alpinus" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCYGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAMCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGAYGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_riparius2" taxon="Thomomys_bottae_riparius" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCSACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_mewa2" taxon="Thomomys_bottae_mewa" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_saxatilis2" taxon="Thomomys_bottae_saxatilis" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGSTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTARGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_bottae_laticeps2" taxon="Thomomys_bottae_laticeps" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACASAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCYTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_talpoides_ocius2" taxon="Thomomys_talpoides_ocius" totalcount="4"
-                  value="CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTATTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTT--------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTC-TATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATCTCTTTGTCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTGTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGTA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A"/>
-        <sequence id="seq_Thomomys_idahoensis_pygmaeus_a2" taxon="Thomomys_idahoensis_pygmaeus_a" totalcount="4"
-                  value="???????TTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTCGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------T--GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGACTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTA--------CCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTA?????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_idahoensis_pygmaeus_b2" taxon="Thomomys_idahoensis_pygmaeus_b" totalcount="4"
-                  value="?ATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTTACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACTAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTATACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATGTTTTTTTT-G------------------------------CACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCACCACTTCTGGCTTTTTTTTTTCTACGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGCTTTTTATTTATGCTTACCTGAAGATTATTGATGATGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATTATGTTTGTGCAA????"/>
-        <sequence id="seq_Thomomys_mazama_mazama2" taxon="Thomomys_mazama_mazama" totalcount="4"
-                  value="??????????????????????A---GCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------------------------------------------------------------------------------TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAAGCACTTTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGTTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTT?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_mazama_nasicus2" taxon="Thomomys_mazama_nasicus" totalcount="4"
-                  value="??????????????GCTTTCTTACGTGCTTATATGCTTGTGTGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGCCAGTAGTGGGTGACACAAATTTCATTTAATTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATATAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCTTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTTGTGCATGCTATGCAGGCACTCTACCACTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATGTTTCGTTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACATCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTGTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTCC---------GGTACCATGCACTGGAACCCAGGTCTTCGTGCATGCTGGACAGCAACTCTACCACTAGGCAAAGCTTCTGGACCCATTAGT?????????????????????????????"/>
-        <sequence id="seq_Thomomys_monticola_a2" taxon="Thomomys_monticola_a" totalcount="4"
-                  value="CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTTGCCAGTCCTGGGCTTGAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGATCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A"/>
-        <sequence id="seq_Thomomys_monticola_b2" taxon="Thomomys_monticola_b" totalcount="4"
-                  value="CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGAGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAAYGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTT--GCCAGTCCTGGGCTTSAGCTCAGGGCCTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTKTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTACCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCACTAGCCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGAYCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCYAGTCCTGGGGCTTGAAATCAGGGTTTGAACATTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------AATACCATGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCATTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A"/>
-        <sequence id="seq_Thomomys_talpoides_yakimensis2" taxon="Thomomys_talpoides_yakimensis" totalcount="4"
-                  value="?????????????????TTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGCTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAGTGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT---------------------------TTTGCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTTTTTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTAGGCAAGCACTCTACCAGTAGGCCAAACTCCCAGCCCCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGTCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAATACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCAC???????????????????????????????????????????????????????"/>
-        <sequence id="seq_Thomomys_talpoides_bridgeri2" taxon="Thomomys_talpoides_bridgeri" totalcount="4"
-                  value="CATGATTTTTTCATGCTTTCTTAC-TGCTTATCTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACACTACTGTCAGTAGTGGGTGACACAAATTTCATTTAATTTGGTTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAACGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCACGATATCTTTTCCAACCCTAGATTTTTTTTTTT------------------------------GCACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCACTTGAGCCTCAGCATCACTTCTGGCTTTTTTT-TTCTATGTATGTGGTATCAAGGAATCGAACCCGGGTCTTCGTGCATGCTCGGCAAGCACTCTACCACTAGGCCAAACTCCCAGCCYCAACCCTAGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTTATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCTTTGGGCTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTTGACTCTTTTC---------GGTACCATGCACTGGAACCCAGGTCTTCATGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATGTTTGTGCAACT-A"/>
-        <sequence id="seq_Thomomys_townsendii_townsendii2" taxon="Thomomys_townsendii_townsendii" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACACAAATTTCATTTAGTTTGGGTGTGTGCCTACCAGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCCTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCAACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGTTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCCACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTT--ATATCATCTTTGTGCAACT-A"/>
-        <sequence id="seq_Thomomys_townsendii_relictus2" taxon="Thomomys_townsendii_relictus" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTATGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGWTTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_umbrinus_chihuahuae2" taxon="Thomomys_umbrinus_chihuahuae" totalcount="4"
-                  value="CATGATTTTGTCATGCTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTTGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTGTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTRCCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTT-ATATCATCTTTGTGAAACT-A"/>
-        <sequence id="seq_Thomomys_umbrinus_atroavarius2" taxon="Thomomys_umbrinus_atroavarius" totalcount="4"
-                  value="CATGATTTTGTCATGYTTTCTTAC-TGCTTATTTGCTTGTGGGCTTTGGGTTGTTTTCACCTGTGGGTYGATTGACGCTACTGTCAGTAGTGGGTGACAGAAATTTCATTTAGTTTGGGTGTGTGCCTACCGGTATAATTGCTGGACCACATGTAGGTCTGTATTAATCTTCTGAAGAATGGTTAGGCCATCTGTGAAATGCTGTACTTCTTTRTGTTCCCGCCATTCTGAGTTCTGATTTCATGATACCTTTTCCACCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGATTTTATGGGGCTCTTTTATGTAACCAGAATGGCAGATG-----TTTCATCTTGGTTTTGATTTATGCTTACCTGAAGATTATTGATGGTGACCTCGATTTCTTGTGCTTTTTAGTGATTTCTTTGCCAGTCCTGGGGCTTGAACTCAGGGTTTGAACACTGTCCTTGGACTTTCTCAAGGCTAGAGCTCTACCATTTGAGCCACAACACCACTTTCGACTCTTTTCTATGTATGTGGTACCGTGCACTGGAACCCAGGTCTTCGTGCATGCTAGACAGCA-CTCTACCACTAGGCCAAACTTCTGGACCCATTAGTGATTTTTYATATCATCTTTGTGAAACT-A"/>
-    </data>
-
-    <plate spec='Plate' var='n' range='.26,.29,.47'>
-        <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
-        <input spec='HKY' id='hky$(n)' kappa='@hky.kappa$(n)'>
-            <frequencies spec='Frequencies' frequencies='@hky.frequencies$(n)'/>
-        </input>
-
-        <!-- site model                                                              -->
-        <input spec='SiteModel' id="siteModel$(n)" substModel='@hky$(n)'/>
-
-        <tree spec='beast.util.ClusterTree' id='tree$(n)' clusterType='upgma' taxa='@alignment$(n)'/>
-
-        <input spec='TreeLikelihood' id="treeLikelihood$(n)"
-               data="@alignment$(n)"
-               tree="@tree$(n)"
-               siteModel="@siteModel$(n)"/>
-
-        <parameter id="hky.kappa$(n)" value="2.0" lower="0.0"/>
-        <parameter id="hky.frequencies$(n)" value="0.25" dimension="4"/>
-    </plate>
-
-    <parameter id="popSizes" value="0.017" lower="0.0"/>
-    <input name="indicators" spec='BooleanParameter' id='indicators' value="false"/>
-    <parameter id="populationMean" value="0.017" lower="0.0"/>
-
-    <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
-        <state>
-            <plate spec='Plate' var='n' range='.26,.29,.47'>
-                <stateNode idref='hky.kappa$(n)'/>
-                <stateNode idref='hky.frequencies$(n)'/>
-                <stateNode idref='tree$(n)'/>
-            </plate>
-            <stateNode idref='popSizes'/>
-            <stateNode idref='indicators'/>
-            <stateNode idref='populationMean'/>
-        </state>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution spec="Prior" x="@populationMean">
-                    <distr offset="0.0" spec="OneOnX"/>
-                </distribution>
-                <distribution spec="Prior">
-                    <x arg="@indicators" id="indsSun" spec="Sum"/>
-                    <distr offset="0.0" spec="Poisson">
-                        <parameter dimension="1" estimate="true" lower="0.0" name="lambda" upper="0.0" value="0.6931471805599453"/>
-                    </distr>
-                </distribution>
-                <distribution id="populationMeanPrior" spec="Prior" x="@popSizes">
-                    <distr id="popPriorDist" mean="@populationMean" offset="0.0" spec="Exponential"/>
-                </distribution>
-
-                <distribution id="coalescent" spec="CompoundDistribution">
-                    <distribution id="Coal.26" spec="Coalescent" treeIntervals="@TreeIntervals.26">
-                        <populationModel id="scaledDemo4" spec="beast.evolution.tree.coalescent.ScaledPopulationFunction">
-                            <population id="demographic" populationIndicators="@indicators" populationSizes="@popSizes"
-                                        spec="beast.evolution.tree.coalescent.CompoundPopulationFunction" type="linear"
-                                        useIntervalsMiddle="false">
-                                <plate spec='Plate' var='n' range='.26,.29,.47'>
-                                    <itree id="TreeIntervals$(n)" spec="TreeIntervals" tree="@tree$(n)"/>
-                                </plate>
-                            </population>
-                            <parameter dimension="1" estimate="true" lower="0.0" name="factor" upper="0.0" value="3"/>
-                        </populationModel>
-                    </distribution>
-
-                    <distribution id="Coal.29" populationModel="@scaledDemo4" spec="Coalescent" treeIntervals="@TreeIntervals.29"/>
-                    <distribution id="Coal.47" populationModel="@scaledDemo4" spec="Coalescent" treeIntervals="@TreeIntervals.47"/>
-                </distribution>
-
-                <plate spec='Plate' var='n' range='.26,.29,.47'>
-                    <distribution spec="Prior" x="@hky.kappa$(n)">
-                        <distr M="1.0" S="1.25" meanInRealSpace="false" spec="LogNormalDistributionModel"/>
-                    </distribution>
-                    <distribution spec="Prior" x="@hky.frequencies$(n)">
-                        <distr lower="0.0" upper="1.0" spec="beast.math.distributions.Uniform"/>
-                    </distribution>
-                </plate>
-            </distribution>
-
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <plate spec='Plate' var='n' range='.26,.29,.47'>
-                    <distribution idref="treeLikelihood$(n)"/>
-                </plate>
-            </distribution>
-        </distribution>
-
-
-        <operator id="bitflip" parameter="@indicators" spec="BitFlipOperator" uniform="true" weight="30.0"/>
-        <operator dist="@popPriorDist" indicators="@indicators" spec="beast.evolution.tree.coalescent.SampleOffValues"
-                  values="@popSizes" weight="15.0"/>
-        <operator degreesOfFreedom="1" indicator="@indicators" parameter="@popSizes" scaleAll="false"
-                  scaleAllIndependently="false" scaleFactor="0.5" spec="ScaleOperator" weight="6.0"/>
-        <operator spec='ScaleOperator' scaleFactor="0.9" weight="3" parameter="@populationMean"/>
-        <operator scaleFactor="0.7" spec="UpDownOperator" weight="30.0">
-            <down idref="popSizes"/>
-            <down idref="populationMean"/>
-            <plate spec='Plate' var='n' range='.26,.29,.47'>
-                <down idref="tree$(n)"/>
-            </plate>
-        </operator>
-
-        <plate spec='Plate' var='n' range='.26,.29,.47'>
-            <operator spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa$(n)"/>
-            <operator spec='DeltaExchangeOperator' delta="0.01" weight="0.1" parameter="@hky.frequencies$(n)"/>
-            <operator spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree$(n)"/>
-            <operator spec='Uniform' weight="30" tree="@tree$(n)"/>
-            <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree$(n)"/>
-            <operator spec='Exchange' isNarrow='true' weight="15" tree="@tree$(n)"/>
-            <operator spec='Exchange' isNarrow='false' weight="3" tree="@tree$(n)"/>
-            <operator spec='WilsonBalding' weight="1" tree="@tree$(n)"/>
-            <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree$(n)"/>
-        </plate>
-
-        <logger logEvery="100000" mode="autodetect">
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log idref="populationMean"/>
-            <log spec="Sum" arg="@indicators"/>
-            <log idref="indicators"/>
-            <plate spec='Plate' var='n' range='.26,.29,.47'>
-                <log spec='beast.evolution.tree.TreeHeightLogger' tree='@tree$(n)'/>
-                <log idref="hky.kappa$(n)"/>
-                <log idref="hky.frequencies$(n)"/>
-                <log idref="treeLikelihood$(n)"/>
-            </plate>
-            <log idref="coalescent"/>
-            <log idref="popSizes"/>
-        </logger>
-
-        <logger fileName="test.$(seed).log" logEvery="1000" mode="autodetect" model="@posterior">
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log idref="populationMean"/>
-            <log spec="Sum" arg="@indicators"/>
-            <log idref="indicators"/>
-            <plate spec='Plate' var='n' range='.26,.29,.47'>
-                <log spec='beast.evolution.tree.TreeHeightLogger' tree='@tree$(n)'/>
-                <log idref="hky.kappa$(n)"/>
-                <log idref="hky.frequencies$(n)"/>
-                <log idref="treeLikelihood$(n)"/>
-            </plate>
-            <log idref="coalescent"/>
-            <log idref="popSizes"/>
-        </logger>
-    </run>
-
-</beast>
diff -Nru beast2-mcmc-2.6.6+dfsg/release/common/README.txt beast2-mcmc-2.6.7+dfsg/release/common/README.txt
--- beast2-mcmc-2.6.6+dfsg/release/common/README.txt	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/common/README.txt	2022-04-04 07:18:36.000000000 +0000
@@ -1,7 +1,7 @@
-                    BEAST v2.6.6 2021
-                 Beast 2 development team 2011-2021
+                    BEAST v2.6.7 2022
+                 Beast 2 development team 2011-2022
 
-Last updated: August 2021
+Last updated: March 2022
 
 Contents:
 1) INTRODUCTION
diff -Nru "/tmp/tmpf4cdn695/LuIOAMVLdw/beast2-mcmc-2.6.6+dfsg/release/common/VERSION HISTORY.txt" "/tmp/tmpf4cdn695/Ko41VIyH3z/beast2-mcmc-2.6.7+dfsg/release/common/VERSION HISTORY.txt"
--- "/tmp/tmpf4cdn695/LuIOAMVLdw/beast2-mcmc-2.6.6+dfsg/release/common/VERSION HISTORY.txt"	2021-08-11 20:11:54.000000000 +0000
+++ "/tmp/tmpf4cdn695/Ko41VIyH3z/beast2-mcmc-2.6.7+dfsg/release/common/VERSION HISTORY.txt"	2022-04-04 07:18:36.000000000 +0000
@@ -1,10 +1,23 @@
-                    BEAST v2.6.6 2021
-                 Beast 2 development team 2011-2021
+                    BEAST v2.6.7 2022
+                 Beast 2 development team 2011-2022
 Version History
-Last updated: August 2021
+Last updated: March 2022
 
 All issues can be viewed at https://github.com/CompEvol/beast2/issues
 ================================================================================
+Version 2.6.7
+	SimulatedAlignment correctly links indices of tree to alignment
+        Option 'ascii' added to Logger to allow it to convert output to ascii or not
+        Loading two dimensional data into trait dialog robustified
+        Make NexusParser more robust and allow Fasta imports to select from all data types
+        Fix TreeAnnotator -heights processing issue
+        Make Prior.sample() obey parameter bounds
+        Fix auto-set clock rate in BEAUti when independent trees are involved
+        Fix TipDateRandomWalker to ensure heights are always >= 0
+        Add upper limit to delta exchange optimization 
+        Made tree input to RatesStatistic required to ensure appropriate behaviour
+        Remove superfluous new lines in XML produced by BEAUti
+
 Version 2.6.6
 	Fix so that when not using ambiguities, the nucleotide 'U' base pair is correctly interpreted
 	Fix tree annotator for lower bound on common ancestor heights
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/applauncher beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/applauncher
--- beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/applauncher	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/applauncher	2022-04-04 07:18:36.000000000 +0000
@@ -1,5 +1,5 @@
 #!/bin/sh
-export JAVA_HOME=$(dirname "$0")/../jre1.8.0_282
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_292
 
 if [ -z "$BEAST" ]; then
 	## resolve links - $0 may be a link to application
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/beast beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/beast
--- beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/beast	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/beast	2022-04-04 07:18:36.000000000 +0000
@@ -1,5 +1,5 @@
 #!/bin/sh
-export JAVA_HOME=$(dirname "$0")/../jre1.8.0_282
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_292
 
 if [ -z "$BEAST" ]; then
 	## resolve links - $0 may be a link to application
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/beauti beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/beauti
--- beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/beauti	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/beauti	2022-04-04 07:18:36.000000000 +0000
@@ -1,5 +1,5 @@
 #!/bin/sh
-export JAVA_HOME=$(dirname "$0")/../jre1.8.0_282
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_292
 
 if [ -z "$BEAST" ]; then
 	## resolve links - $0 may be a link to application
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/densitree beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/densitree
--- beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/densitree	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/densitree	2022-04-04 07:18:36.000000000 +0000
@@ -1,5 +1,5 @@
 #!/bin/sh
-export JAVA_HOME=$(dirname "$0")/../jre1.8.0_282
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_292
 
 if [ -z "$BEAST" ]; then
 	## resolve links - $0 may be a link to application
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/loganalyser beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/loganalyser
--- beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/loganalyser	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/loganalyser	2022-04-04 07:18:36.000000000 +0000
@@ -1,5 +1,5 @@
 #!/bin/sh
-export JAVA_HOME=$(dirname "$0")/../jre1.8.0_282
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_292
 
 if [ -z "$BEAST" ]; then
 	## resolve links - $0 may be a link to application
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/logcombiner beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/logcombiner
--- beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/logcombiner	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/logcombiner	2022-04-04 07:18:36.000000000 +0000
@@ -1,5 +1,5 @@
 #!/bin/sh
-export JAVA_HOME=$(dirname "$0")/../jre1.8.0_282
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_292
 
 if [ -z "$BEAST" ]; then
 	## resolve links - $0 may be a link to application
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/packagemanager beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/packagemanager
--- beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/packagemanager	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/packagemanager	2022-04-04 07:18:36.000000000 +0000
@@ -1,5 +1,5 @@
 #!/bin/sh
-export JAVA_HOME=$(dirname "$0")/../jre1.8.0_282
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_292
 
 if [ -z "$BEAST" ]; then
 	## resolve links - $0 may be a link to application
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/treeannotator beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/treeannotator
--- beast2-mcmc-2.6.6+dfsg/release/Linux/jrebin/treeannotator	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Linux/jrebin/treeannotator	2022-04-04 07:18:36.000000000 +0000
@@ -1,5 +1,5 @@
 #!/bin/sh
-export JAVA_HOME=$(dirname "$0")/../jre1.8.0_282
+export JAVA_HOME=$(dirname "$0")/../jre1.8.0_292
 
 if [ -z "$BEAST" ]; then
 	## resolve links - $0 may be a link to application
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Mac/createdmg.sh beast2-mcmc-2.6.7+dfsg/release/Mac/createdmg.sh
--- beast2-mcmc-2.6.6+dfsg/release/Mac/createdmg.sh	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Mac/createdmg.sh	2022-04-04 07:18:36.000000000 +0000
@@ -15,12 +15,13 @@
 
 cp install.png ${source}/${backgroundPictureName}
 
+echo "Creating image from folder ${source} at volume name ${title}"
 hdiutil create -srcfolder "${source}" -volname "${title}" -fs HFS+ \
       -fsargs "-c c=64,a=16,e=16" -format UDRW -size ${size}k pack.temp.dmg
 
 export device=$(hdiutil attach -readwrite -noverify -noautoopen "pack.temp.dmg" | \
          egrep '^/dev/' | sed 1q | awk '{print $1}')
-
+echo "Attach device : ${device}"
 
 echo '
    tell application "Finder"
@@ -54,5 +55,6 @@
 sync
 sync
 hdiutil detach ${device}
+echo "Detach device : ${device}"
 hdiutil convert "pack.temp.dmg" -format UDZO -imagekey zlib-level=9 -o "${finalDMGName}"
 rm -f /pack.temp.dmg 
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Mac/stub/3-0-3/universalJavaApplicationJREStub beast2-mcmc-2.6.7+dfsg/release/Mac/stub/3-0-3/universalJavaApplicationJREStub
--- beast2-mcmc-2.6.6+dfsg/release/Mac/stub/3-0-3/universalJavaApplicationJREStub	1970-01-01 00:00:00.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Mac/stub/3-0-3/universalJavaApplicationJREStub	2022-04-04 07:18:36.000000000 +0000
@@ -0,0 +1,572 @@
+#!/bin/bash
+##################################################################################
+#                                                                                #
+# universalJavaApplicationStub                                                   #
+#                                                                                #
+# A BASH based JavaApplicationStub for Java Apps on Mac OS X                     #
+# that works with both Apple's and Oracle's plist format.                        #
+#                                                                                #
+# Inspired by Ian Roberts stackoverflow answer                                   #
+# at http://stackoverflow.com/a/17546508/1128689                                 #
+#                                                                                #
+# @author    Tobias Fischer                                                      #
+# @url       https://github.com/tofi86/universalJavaApplicationStub              #
+# @date      2018-07-29                                                          #
+# @version   3.0.3                                                               #
+#                                                                                #
+##################################################################################
+#                                                                                #
+# The MIT License (MIT)                                                          #
+#                                                                                #
+# Copyright (c) 2014-2018 Tobias Fischer                                         #
+#                                                                                #
+# Permission is hereby granted, free of charge, to any person obtaining a copy   #
+# of this software and associated documentation files (the "Software"), to deal  #
+# in the Software without restriction, including without limitation the rights   #
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell      #
+# copies of the Software, and to permit persons to whom the Software is          #
+# furnished to do so, subject to the following conditions:                       #
+#                                                                                #
+# The above copyright notice and this permission notice shall be included in all #
+# copies or substantial portions of the Software.                                #
+#                                                                                #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR     #
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,       #
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE    #
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER         #
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  #
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE  #
+# SOFTWARE.                                                                      #
+#                                                                                #
+##################################################################################
+
+
+
+# function 'stub_logger()'
+#
+# A logger which logs to the macOS Console.app using the 'syslog' command
+#
+# @param1  the log message
+# @return  void
+################################################################################
+function stub_logger() {
+	syslog -s -k \
+		Facility com.apple.console \
+		Level Notice \
+		Sender "$(basename "$0")" \
+		Message "[$$][${CFBundleName:-$(basename "$0")}] $1"
+}
+
+
+
+# set the directory abspath of the current
+# shell script with symlinks being resolved
+############################################
+
+PRG=$0
+while [ -h "$PRG" ]; do
+	ls=$(ls -ld "$PRG")
+	link=$(expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null)
+	if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+		PRG="$link"
+	else
+		PRG="$(dirname "$PRG")/$link"
+	fi
+done
+PROGDIR=$(dirname "$PRG")
+stub_logger "[StubDir] $PROGDIR"
+
+
+
+# set files and folders
+############################################
+
+# the absolute path of the app package
+cd "$PROGDIR"/../../ || exit 11
+AppPackageFolder=$(pwd)
+
+# the base path of the app package
+cd .. || exit 12
+AppPackageRoot=$(pwd)
+
+# set Apple's Java folder
+AppleJavaFolder="${AppPackageFolder}"/Contents/Resources/Java
+
+# set Apple's Resources folder
+AppleResourcesFolder="${AppPackageFolder}"/Contents/Resources
+
+# set Oracle's Java folder
+OracleJavaFolder="${AppPackageFolder}"/Contents/Java
+
+# set Oracle's Resources folder
+OracleResourcesFolder="${AppPackageFolder}"/Contents/Resources
+
+# set path to Info.plist in bundle
+InfoPlistFile="${AppPackageFolder}"/Contents/Info.plist
+
+# set the default JVM Version to a null string
+JVMVersion=""
+JVMMaxVersion=""
+
+
+
+# function 'plist_get()'
+#
+# read a specific Plist key with 'PlistBuddy' utility
+#
+# @param1  the Plist key with leading colon ':'
+# @return  the value as String or Array
+################################################################################
+plist_get(){
+	/usr/libexec/PlistBuddy -c "print $1" "${InfoPlistFile}" 2> /dev/null
+}
+
+# function 'plist_get_java()'
+#
+# read a specific Plist key with 'PlistBuddy' utility
+# in the 'Java' or 'JavaX' dictionary (<dict>)
+#
+# @param1  the Plist :Java(X):Key with leading colon ':'
+# @return  the value as String or Array
+################################################################################
+plist_get_java(){
+	plist_get ${JavaKey:-":Java"}$1
+}
+
+
+
+# read Info.plist and extract JVM options
+############################################
+
+# read the program name from CFBundleName
+CFBundleName=$(plist_get ':CFBundleName')
+
+# read the icon file name
+CFBundleIconFile=$(plist_get ':CFBundleIconFile')
+
+
+# check Info.plist for Apple style Java keys -> if key :Java is present, parse in apple mode
+/usr/libexec/PlistBuddy -c "print :Java" "${InfoPlistFile}" > /dev/null 2>&1
+exitcode=$?
+JavaKey=":Java"
+
+# if no :Java key is present, check Info.plist for universalJavaApplication style JavaX keys -> if key :JavaX is present, parse in apple mode
+if [ $exitcode -ne 0 ]; then
+	/usr/libexec/PlistBuddy -c "print :JavaX" "${InfoPlistFile}" > /dev/null 2>&1
+	exitcode=$?
+	JavaKey=":JavaX"
+fi
+
+
+# read 'Info.plist' file in Apple style if exit code returns 0 (true, ':Java' key is present)
+if [ $exitcode -eq 0 ]; then
+	stub_logger "[PlistStyle] Apple"
+
+	# set Java and Resources folder
+	JavaFolder="${AppleJavaFolder}"
+	ResourcesFolder="${AppleResourcesFolder}"
+
+	APP_PACKAGE="${AppPackageFolder}"
+	JAVAROOT="${AppleJavaFolder}"
+	USER_HOME="$HOME"
+
+
+	# read the Java WorkingDirectory
+	JVMWorkDir=$(plist_get_java ':WorkingDirectory' | xargs)
+	# set Working Directory based upon PList value
+	if [[ ! -z ${JVMWorkDir} ]]; then
+		WorkingDirectory="${JVMWorkDir}"
+	else
+		# AppPackageRoot is the standard WorkingDirectory when the script is started
+		WorkingDirectory="${AppPackageRoot}"
+	fi
+	# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
+	WorkingDirectory=$(eval echo "${WorkingDirectory}")
+
+
+	# read the MainClass name
+	JVMMainClass="$(plist_get_java ':MainClass')"
+
+	# read the SplashFile name
+	JVMSplashFile=$(plist_get_java ':SplashFile')
+
+	# read the JVM Properties as an array and retain spaces
+	IFS=$'\t\n'
+	JVMOptions=($(xargs -n1 <<<$(plist_get_java ':Properties' | grep " =" | sed 's/^ */-D/g' | sed -E 's/ = (.*)$/="\1"/g')))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the ClassPath in either Array or String style
+	JVMClassPath_RAW=$(plist_get_java ':ClassPath' | xargs)
+	if [[ $JVMClassPath_RAW == *Array* ]] ; then
+		JVMClassPath=.$(plist_get_java ':ClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
+	else
+		JVMClassPath=${JVMClassPath_RAW}
+	fi
+	# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
+	JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	# read the JVM Options in either Array or String style
+	JVMDefaultOptions_RAW=$(plist_get_java ':VMOptions' | xargs)
+	if [[ $JVMDefaultOptions_RAW == *Array* ]] ; then
+		JVMDefaultOptions=$(plist_get_java ':VMOptions' | grep "    " | sed 's/^ */ /g' | tr -d '\n' | xargs)
+	else
+		JVMDefaultOptions=${JVMDefaultOptions_RAW}
+	fi
+
+	# read StartOnMainThread and add as -XstartOnFirstThread
+	JVMStartOnMainThread=$(plist_get_java ':StartOnMainThread')
+	if [ "${JVMStartOnMainThread}" == "true" ]; then
+		JVMDefaultOptions+=" -XstartOnFirstThread"
+	fi
+
+	# read the JVM Arguments as an array and retain spaces
+	IFS=$'\t\n'
+	MainArgs=($(xargs -n1 <<<$(plist_get_java ':Arguments')))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the Java version we want to find
+	JVMVersion=$(plist_get_java ':JVMVersion' | xargs)
+	# post processing of the version string follows below...
+
+
+# read 'Info.plist' file in Oracle style
+else
+	stub_logger "[PlistStyle] Oracle"
+
+	# set Working Directory and Java and Resources folder
+	JavaFolder="${OracleJavaFolder}"
+	ResourcesFolder="${OracleResourcesFolder}"
+	WorkingDirectory="${OracleJavaFolder}"
+
+	APP_ROOT="${AppPackageFolder}"
+
+	# read the MainClass name
+	JVMMainClass="$(plist_get ':JVMMainClassName')"
+
+	# read the SplashFile name
+	JVMSplashFile=$(plist_get ':JVMSplashFile')
+
+	# read the JVM Options as an array and retain spaces
+	IFS=$'\t\n'
+	JVMOptions=($(plist_get ':JVMOptions' | grep "    " | sed 's/^ *//g'))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the ClassPath in either Array or String style
+	JVMClassPath_RAW=$(plist_get ':JVMClassPath')
+	if [[ $JVMClassPath_RAW == *Array* ]] ; then
+		JVMClassPath=.$(plist_get ':JVMClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
+		# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
+		JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	elif [[ ! -z ${JVMClassPath_RAW} ]] ; then
+		JVMClassPath=${JVMClassPath_RAW}
+		# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
+		JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	else
+		#default: fallback to OracleJavaFolder
+		JVMClassPath="${JavaFolder}/*"
+		# Do NOT expand the default 'AppName.app/Contents/Java/*' classpath (#42)
+	fi
+
+	# read the JVM Default Options
+	JVMDefaultOptions=$(plist_get ':JVMDefaultOptions' | grep -o " \-.*" | tr -d '\n' | xargs)
+
+	# read the Main Arguments from JVMArguments key as an array and retain spaces (see #46 for naming details)
+	IFS=$'\t\n'
+	MainArgs=($(xargs -n1 <<<$(plist_get ':JVMArguments' | tr -d '\n' | sed -E 's/Array \{ *(.*) *\}/\1/g' | sed 's/  */ /g')))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the Java version we want to find
+	JVMVersion=$(plist_get ':JVMVersion' | xargs)
+	# post processing of the version string follows below...
+fi
+
+
+
+# JVMVersion: post processing and optional splitting
+if [[ ${JVMVersion} == *";"* ]]; then
+	minMaxArray=(${JVMVersion//;/ })
+	JVMVersion=${minMaxArray[0]//+}
+	JVMMaxVersion=${minMaxArray[1]//+}
+fi
+stub_logger "[JavaRequirement] JVM minimum version: ${JVMVersion}"
+stub_logger "[JavaRequirement] JVM maximum version: ${JVMMaxVersion}"
+
+# MainArgs: replace occurences of $APP_ROOT with its content
+MainArgsArr=()
+for i in "${MainArgs[@]}"
+do
+	MainArgsArr+=("$(eval echo "$i")")
+done
+
+# JVMOptions: replace occurences of $APP_ROOT with its content
+JVMOptionsArr=()
+for i in "${JVMOptions[@]}"
+do
+	JVMOptionsArr+=("$(eval echo "$i")")
+done
+
+
+# internationalized messages
+############################################
+
+LANG=$(defaults read -g AppleLocale)
+stub_logger "[Language] $LANG"
+
+# French localization
+if [[ $LANG == fr* ]] ; then
+	MSG_ERROR_LAUNCHING="ERREUR au lancement de '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="'MainClass' n'est pas spécifié.\nL'application Java ne peut pas être lancée."
+	MSG_JVMVERSION_REQ_INVALID="La syntaxe de la version Java demandée est invalide: %s\nVeuillez contacter le développeur de l'application."
+	MSG_NO_SUITABLE_JAVA="La version de Java installée sur votre système ne convient pas.\nCe programme nécessite Java %s"
+	MSG_JAVA_VERSION_OR_LATER="ou ultérieur"
+	MSG_JAVA_VERSION_LATEST="(dernière mise à jour)"
+	MSG_JAVA_VERSION_MAX="à %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Merci de bien vouloir installer la version de Java requise."
+	MSG_INSTALL_JAVA="Java doit être installé sur votre système.\nRendez-vous sur java.com et suivez les instructions d'installation..."
+	MSG_LATER="Plus tard"
+	MSG_VISIT_JAVA_DOT_COM="Visiter java.com"
+
+# German localization
+elif [[ $LANG == de* ]] ; then
+	MSG_ERROR_LAUNCHING="FEHLER beim Starten von '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="Die 'MainClass' ist nicht spezifiziert!\nDie Java-Anwendung kann nicht gestartet werden!"
+	MSG_JVMVERSION_REQ_INVALID="Die Syntax der angeforderten Java-Version ist ungültig: %s\nBitte kontaktieren Sie den Entwickler der App."
+	MSG_NO_SUITABLE_JAVA="Es wurde keine passende Java-Version auf Ihrem System gefunden!\nDieses Programm benötigt Java %s"
+	MSG_JAVA_VERSION_OR_LATER="oder neuer"
+	MSG_JAVA_VERSION_LATEST="(neuste Unterversion)"
+	MSG_JAVA_VERSION_MAX="bis %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Stellen Sie sicher, dass die angeforderte Java-Version installiert ist."
+	MSG_INSTALL_JAVA="Auf Ihrem System muss die 'Java'-Software installiert sein.\nBesuchen Sie java.com für weitere Installationshinweise."
+	MSG_LATER="Später"
+	MSG_VISIT_JAVA_DOT_COM="java.com öffnen"
+
+# Simplifyed Chinese localization
+elif [[ $LANG == zh* ]] ; then
+	MSG_ERROR_LAUNCHING="无法启动 '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="没有指定 'MainClass'！\nJava程序无法启动!"
+	MSG_JVMVERSION_REQ_INVALID="Java版本参数语法错误: %s\n请联系该应用的开发者。"
+	MSG_NO_SUITABLE_JAVA="没有在系统中找到合适的Java版本！\n必须安装Java %s才能够使用该程序！"
+	MSG_JAVA_VERSION_OR_LATER="及以上版本"
+	MSG_JAVA_VERSION_LATEST="（最新版本）"
+	MSG_JAVA_VERSION_MAX="最高为 %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="请确保系统中安装了所需的Java版本"
+	MSG_INSTALL_JAVA="你需要在Mac中安装Java运行环境！\n访问 java.com 了解如何安装。"
+	MSG_LATER="稍后"
+	MSG_VISIT_JAVA_DOT_COM="访问 java.com"
+
+# English default localization
+else
+	MSG_ERROR_LAUNCHING="ERROR launching '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="'MainClass' isn't specified!\nJava application cannot be started!"
+	MSG_JVMVERSION_REQ_INVALID="The syntax of the required Java version is invalid: %s\nPlease contact the App developer."
+	MSG_NO_SUITABLE_JAVA="No suitable Java version found on your system!\nThis program requires Java %s"
+	MSG_JAVA_VERSION_OR_LATER="or later"
+	MSG_JAVA_VERSION_LATEST="(latest update)"
+	MSG_JAVA_VERSION_MAX="up to %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Make sure you install the required Java version."
+	MSG_INSTALL_JAVA="You need to have JAVA installed on your Mac!\nVisit java.com for installation instructions..."
+	MSG_LATER="Later"
+	MSG_VISIT_JAVA_DOT_COM="Visit java.com"
+fi
+
+
+
+# function 'get_java_version_from_cmd()'
+#
+# returns Java version string from 'java -version' command
+# works for both old (1.8) and new (9) version schema
+#
+# @param1  path to a java JVM executable
+# @return  the Java version number as displayed in 'java -version' command
+################################################################################
+function get_java_version_from_cmd() {
+	# second sed command strips " and -ea from the version string
+	echo $("$1" -version 2>&1 | awk '/version/{print $3}' | sed -E 's/"//g;s/-ea//g')
+}
+
+
+# function 'extract_java_major_version()'
+#
+# extract Java major version from a version string
+#
+# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
+# @return  the major version (e.g. '7', '8' or '9', etc.)
+################################################################################
+function extract_java_major_version() {
+	echo $(echo "$1" | sed -E 's/^1\.//;s/^([0-9]+)(-ea|(\.[0-9_.]{1,7})?)(-b[0-9]+-[0-9]+)?[+*]?$/\1/')
+}
+
+
+# function 'get_comparable_java_version()'
+#
+# return comparable version for a Java version number or requirement string
+#
+# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
+# @return  an 8 digit numeral ('1.8.0_45'->'08000045'; '9.1.13'->'09001013')
+################################################################################
+function get_comparable_java_version() {
+	# cleaning: 1) remove leading '1.'; 2) remove build string (e.g. '-b14-468'); 3) remove 'a-Z' and '-*+' (e.g. '-ea'); 4) replace '_' with '.'
+	local cleaned=$(echo "$1" | sed -E 's/^1\.//g;s/-b[0-9]+-[0-9]+$//g;s/[a-zA-Z+*\-]//g;s/_/./g')
+	# splitting at '.' into an array
+	local arr=( ${cleaned//./ } )
+	# echo a string with left padded version numbers
+	echo "$(printf '%02s' ${arr[0]})$(printf '%03s' ${arr[1]})$(printf '%03s' ${arr[2]})"
+}
+
+
+# function 'is_valid_requirement_pattern()'
+#
+# check whether the Java requirement is a valid requirement pattern
+#
+# supported requirements are for example:
+# - 1.6       requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6*      requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6+      requires Java 6 or higher         [1.6, 1.6.0_45, 1.8, 9, etc.]
+# - 1.6.0     requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6.0_45  requires Java 6u45                [1.6.0_45]
+# - 1.6.0_45+ requires Java 6u45 or higher      [1.6.0_45, 1.6.0_88, 1.8, etc.]
+# - 9         requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
+# - 9*        requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
+# - 9+        requires Java 9 or higher         [9.0, 9.1, 10, etc.]
+# - 9.1       requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
+# - 9.1*      requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
+# - 9.1+      requires Java 9.1 or higher       [9.1, 9.2, 10, etc.]
+# - 9.1.3     requires Java 9.1.3               [9.1.3]
+# - 9.1.3*    requires Java 9.1.3 (any update)  [9.1.3]
+# - 9.1.3+    requires Java 9.1.3 or higher     [9.1.3, 9.1.4, 9.2.*, 10, etc.]
+# - 10-ea     requires Java 10 (early access release)
+#
+# unsupported requirement patterns are for example:
+# - 1.2, 1.3, 1.9       Java 2, 3 are not supported
+# - 1.9                 Java 9 introduced a new versioning scheme
+# - 6u45                known versioning syntax, but unsupported
+# - 9-ea*, 9-ea+        early access releases paired with */+
+# - 9., 9.*, 9.+        version ending with a .
+# - 9.1., 9.1.*, 9.1.+  version ending with a .
+# - 9.3.5.6             4 part version number is unsupported
+#
+# @param1  a Java requirement string ('1.8+')
+# @return  boolean exit code: 0 (is valid), 1 (is not valid)
+################################################################################
+function is_valid_requirement_pattern() {
+	local java_req=$1
+	java8pattern='1\.[4-8](\.0)?(\.0_[0-9]+)?[*+]?'
+	java9pattern='(9|1[0-9])(-ea|[*+]|(\.[0-9]+){1,2}[*+]?)?'
+	# test matches either old Java versioning scheme (up to 1.8) or new scheme (starting with 9)
+	if [[ ${java_req} =~ ^(${java8pattern}|${java9pattern})$ ]]; then
+		return 0
+	else
+		return 1
+	fi
+}
+
+
+
+# determine which JVM to use
+############################################
+
+JAVACMD="${AppPackageFolder}/../jre1.8.0_292/bin/java"
+
+
+# log the Java Command and the extracted version number
+stub_logger "[JavaCommand] '$JAVACMD'"
+stub_logger "[JavaVersion] $(get_java_version_from_cmd "${JAVACMD}")${JAVACMD_version:+ / $JAVACMD_version}"
+
+
+
+if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then
+
+	# different error messages when a specific JVM was required
+	if [ ! -z "${JVMVersion}" ] ; then
+		# display human readable java version (#28)
+		java_version_hr=$(echo ${JVMVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+/ ${MSG_JAVA_VERSION_OR_LATER}/;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
+		MSG_NO_SUITABLE_JAVA_EXPANDED=$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}").
+
+		if [ ! -z "${JVMMaxVersion}" ] ; then
+			java_version_hr=$(extract_java_major_version ${JVMVersion})
+			java_version_max_hr=$(echo ${JVMMaxVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+//;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
+			MSG_NO_SUITABLE_JAVA_EXPANDED="$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}") $(printf "${MSG_JAVA_VERSION_MAX}" "${java_version_max_hr}")"
+		fi
+
+		# log exit cause
+		stub_logger "[EXIT 3] ${MSG_NO_SUITABLE_JAVA_EXPANDED}"
+
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_NO_SUITABLE_JAVA_EXPANDED}\n${MSG_NO_SUITABLE_JAVA_CHECK}\" with title \"${CFBundleName}\"  buttons {\" OK \", \"${MSG_VISIT_JAVA_DOT_COM}\"} default button \"${MSG_VISIT_JAVA_DOT_COM}\" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" \
+				-e "set response to button returned of the result" \
+				-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"http://java.com\""
+		# exit with error
+		exit 3
+
+	else
+		# log exit cause
+		stub_logger "[EXIT 1] ${MSG_ERROR_LAUNCHING}"
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_INSTALL_JAVA}\" with title \"${CFBundleName}\" buttons {\"${MSG_LATER}\", \"${MSG_VISIT_JAVA_DOT_COM}\"} default button \"${MSG_VISIT_JAVA_DOT_COM}\" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" \
+					-e "set response to button returned of the result" \
+					-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"http://java.com\""
+		# exit with error
+		exit 1
+	fi
+fi
+
+
+
+# MainClass check
+############################################
+
+if [ -z "${JVMMainClass}" ]; then
+	# log exit cause
+	stub_logger "[EXIT 2] ${MSG_MISSING_MAINCLASS}"
+	# display error message with AppleScript
+	osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_MISSING_MAINCLASS}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
+	# exit with error
+	exit 2
+fi
+
+
+
+# execute $JAVACMD and do some preparation
+############################################
+
+# enable drag&drop to the dock icon
+export CFProcessPath="$0"
+
+# remove Apples ProcessSerialNumber from passthru arguments (#39)
+if [[ "$*" == -psn* ]] ; then
+	ArgsPassthru=()
+else
+	ArgsPassthru=("$@")
+fi
+
+# change to Working Directory based upon Apple/Oracle Plist info
+cd "${WorkingDirectory}" || exit 13
+stub_logger "[WorkingDirectory] ${WorkingDirectory}"
+
+# execute Java and set
+# - classpath
+# - splash image
+# - dock icon
+# - app name
+# - JVM options / properties (-D)
+# - JVM default options (-X)
+# - main class
+# - main class arguments
+# - passthrough arguments from Terminal or Drag'n'Drop to Finder icon
+stub_logger "[Exec] \"$JAVACMD\" -cp \"${JVMClassPath}\" -splash:\"${ResourcesFolder}/${JVMSplashFile}\" -Xdock:icon=\"${ResourcesFolder}/${CFBundleIconFile}\" -Xdock:name=\"${CFBundleName}\" ${JVMOptionsArr:+$(printf "'%s' " "${JVMOptionsArr[@]}") }${JVMDefaultOptions:+$JVMDefaultOptions }${JVMMainClass}${MainArgsArr:+ $(printf "'%s' " "${MainArgsArr[@]}")}${ArgsPassthru:+ $(printf "'%s' " "${ArgsPassthru[@]}")}"
+exec "${JAVACMD}" \
+		-cp "${JVMClassPath}" \
+		-splash:"${ResourcesFolder}/${JVMSplashFile}" \
+		-Xdock:icon="${ResourcesFolder}/${CFBundleIconFile}" \
+		-Xdock:name="${CFBundleName}" \
+		${JVMOptions:+"${JVMOptions[@]}" }\
+		${JVMDefaultOptions:+$JVMDefaultOptions }\
+		"${JVMMainClass}"\
+		${MainArgsArr:+ "${MainArgsArr[@]}"}\
+		${ArgsPassthru:+ "${ArgsPassthru[@]}"}
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Mac/stub/3-0-3/universalJavaApplicationStub beast2-mcmc-2.6.7+dfsg/release/Mac/stub/3-0-3/universalJavaApplicationStub
--- beast2-mcmc-2.6.6+dfsg/release/Mac/stub/3-0-3/universalJavaApplicationStub	1970-01-01 00:00:00.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Mac/stub/3-0-3/universalJavaApplicationStub	2022-04-04 07:18:36.000000000 +0000
@@ -0,0 +1,774 @@
+#!/bin/bash
+##################################################################################
+#                                                                                #
+# universalJavaApplicationStub                                                   #
+#                                                                                #
+# A BASH based JavaApplicationStub for Java Apps on Mac OS X                     #
+# that works with both Apple's and Oracle's plist format.                        #
+#                                                                                #
+# Inspired by Ian Roberts stackoverflow answer                                   #
+# at http://stackoverflow.com/a/17546508/1128689                                 #
+#                                                                                #
+# @author    Tobias Fischer                                                      #
+# @url       https://github.com/tofi86/universalJavaApplicationStub              #
+# @date      2018-07-29                                                          #
+# @version   3.0.3                                                               #
+#                                                                                #
+##################################################################################
+#                                                                                #
+# The MIT License (MIT)                                                          #
+#                                                                                #
+# Copyright (c) 2014-2018 Tobias Fischer                                         #
+#                                                                                #
+# Permission is hereby granted, free of charge, to any person obtaining a copy   #
+# of this software and associated documentation files (the "Software"), to deal  #
+# in the Software without restriction, including without limitation the rights   #
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell      #
+# copies of the Software, and to permit persons to whom the Software is          #
+# furnished to do so, subject to the following conditions:                       #
+#                                                                                #
+# The above copyright notice and this permission notice shall be included in all #
+# copies or substantial portions of the Software.                                #
+#                                                                                #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR     #
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,       #
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE    #
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER         #
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  #
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE  #
+# SOFTWARE.                                                                      #
+#                                                                                #
+##################################################################################
+
+
+
+# function 'stub_logger()'
+#
+# A logger which logs to the macOS Console.app using the 'syslog' command
+#
+# @param1  the log message
+# @return  void
+################################################################################
+function stub_logger() {
+	syslog -s -k \
+		Facility com.apple.console \
+		Level Notice \
+		Sender "$(basename "$0")" \
+		Message "[$$][${CFBundleName:-$(basename "$0")}] $1"
+}
+
+
+
+# set the directory abspath of the current
+# shell script with symlinks being resolved
+############################################
+
+PRG=$0
+while [ -h "$PRG" ]; do
+	ls=$(ls -ld "$PRG")
+	link=$(expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null)
+	if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+		PRG="$link"
+	else
+		PRG="$(dirname "$PRG")/$link"
+	fi
+done
+PROGDIR=$(dirname "$PRG")
+stub_logger "[StubDir] $PROGDIR"
+
+
+
+# set files and folders
+############################################
+
+# the absolute path of the app package
+cd "$PROGDIR"/../../ || exit 11
+AppPackageFolder=$(pwd)
+
+# the base path of the app package
+cd .. || exit 12
+AppPackageRoot=$(pwd)
+
+# set Apple's Java folder
+AppleJavaFolder="${AppPackageFolder}"/Contents/Resources/Java
+
+# set Apple's Resources folder
+AppleResourcesFolder="${AppPackageFolder}"/Contents/Resources
+
+# set Oracle's Java folder
+OracleJavaFolder="${AppPackageFolder}"/Contents/Java
+
+# set Oracle's Resources folder
+OracleResourcesFolder="${AppPackageFolder}"/Contents/Resources
+
+# set path to Info.plist in bundle
+InfoPlistFile="${AppPackageFolder}"/Contents/Info.plist
+
+# set the default JVM Version to a null string
+JVMVersion=""
+JVMMaxVersion=""
+
+
+
+# function 'plist_get()'
+#
+# read a specific Plist key with 'PlistBuddy' utility
+#
+# @param1  the Plist key with leading colon ':'
+# @return  the value as String or Array
+################################################################################
+plist_get(){
+	/usr/libexec/PlistBuddy -c "print $1" "${InfoPlistFile}" 2> /dev/null
+}
+
+# function 'plist_get_java()'
+#
+# read a specific Plist key with 'PlistBuddy' utility
+# in the 'Java' or 'JavaX' dictionary (<dict>)
+#
+# @param1  the Plist :Java(X):Key with leading colon ':'
+# @return  the value as String or Array
+################################################################################
+plist_get_java(){
+	plist_get ${JavaKey:-":Java"}$1
+}
+
+
+
+# read Info.plist and extract JVM options
+############################################
+
+# read the program name from CFBundleName
+CFBundleName=$(plist_get ':CFBundleName')
+
+# read the icon file name
+CFBundleIconFile=$(plist_get ':CFBundleIconFile')
+
+
+# check Info.plist for Apple style Java keys -> if key :Java is present, parse in apple mode
+/usr/libexec/PlistBuddy -c "print :Java" "${InfoPlistFile}" > /dev/null 2>&1
+exitcode=$?
+JavaKey=":Java"
+
+# if no :Java key is present, check Info.plist for universalJavaApplication style JavaX keys -> if key :JavaX is present, parse in apple mode
+if [ $exitcode -ne 0 ]; then
+	/usr/libexec/PlistBuddy -c "print :JavaX" "${InfoPlistFile}" > /dev/null 2>&1
+	exitcode=$?
+	JavaKey=":JavaX"
+fi
+
+
+# read 'Info.plist' file in Apple style if exit code returns 0 (true, ':Java' key is present)
+if [ $exitcode -eq 0 ]; then
+	stub_logger "[PlistStyle] Apple"
+
+	# set Java and Resources folder
+	JavaFolder="${AppleJavaFolder}"
+	ResourcesFolder="${AppleResourcesFolder}"
+
+	APP_PACKAGE="${AppPackageFolder}"
+	JAVAROOT="${AppleJavaFolder}"
+	USER_HOME="$HOME"
+
+
+	# read the Java WorkingDirectory
+	JVMWorkDir=$(plist_get_java ':WorkingDirectory' | xargs)
+	# set Working Directory based upon PList value
+	if [[ ! -z ${JVMWorkDir} ]]; then
+		WorkingDirectory="${JVMWorkDir}"
+	else
+		# AppPackageRoot is the standard WorkingDirectory when the script is started
+		WorkingDirectory="${AppPackageRoot}"
+	fi
+	# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
+	WorkingDirectory=$(eval echo "${WorkingDirectory}")
+
+
+	# read the MainClass name
+	JVMMainClass="$(plist_get_java ':MainClass')"
+
+	# read the SplashFile name
+	JVMSplashFile=$(plist_get_java ':SplashFile')
+
+	# read the JVM Properties as an array and retain spaces
+	IFS=$'\t\n'
+	JVMOptions=($(xargs -n1 <<<$(plist_get_java ':Properties' | grep " =" | sed 's/^ */-D/g' | sed -E 's/ = (.*)$/="\1"/g')))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the ClassPath in either Array or String style
+	JVMClassPath_RAW=$(plist_get_java ':ClassPath' | xargs)
+	if [[ $JVMClassPath_RAW == *Array* ]] ; then
+		JVMClassPath=.$(plist_get_java ':ClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
+	else
+		JVMClassPath=${JVMClassPath_RAW}
+	fi
+	# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
+	JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	# read the JVM Options in either Array or String style
+	JVMDefaultOptions_RAW=$(plist_get_java ':VMOptions' | xargs)
+	if [[ $JVMDefaultOptions_RAW == *Array* ]] ; then
+		JVMDefaultOptions=$(plist_get_java ':VMOptions' | grep "    " | sed 's/^ */ /g' | tr -d '\n' | xargs)
+	else
+		JVMDefaultOptions=${JVMDefaultOptions_RAW}
+	fi
+
+	# read StartOnMainThread and add as -XstartOnFirstThread
+	JVMStartOnMainThread=$(plist_get_java ':StartOnMainThread')
+	if [ "${JVMStartOnMainThread}" == "true" ]; then
+		JVMDefaultOptions+=" -XstartOnFirstThread"
+	fi
+
+	# read the JVM Arguments as an array and retain spaces
+	IFS=$'\t\n'
+	MainArgs=($(xargs -n1 <<<$(plist_get_java ':Arguments')))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the Java version we want to find
+	JVMVersion=$(plist_get_java ':JVMVersion' | xargs)
+	# post processing of the version string follows below...
+
+
+# read 'Info.plist' file in Oracle style
+else
+	stub_logger "[PlistStyle] Oracle"
+
+	# set Working Directory and Java and Resources folder
+	JavaFolder="${OracleJavaFolder}"
+	ResourcesFolder="${OracleResourcesFolder}"
+	WorkingDirectory="${OracleJavaFolder}"
+
+	APP_ROOT="${AppPackageFolder}"
+
+	# read the MainClass name
+	JVMMainClass="$(plist_get ':JVMMainClassName')"
+
+	# read the SplashFile name
+	JVMSplashFile=$(plist_get ':JVMSplashFile')
+
+	# read the JVM Options as an array and retain spaces
+	IFS=$'\t\n'
+	JVMOptions=($(plist_get ':JVMOptions' | grep "    " | sed 's/^ *//g'))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the ClassPath in either Array or String style
+	JVMClassPath_RAW=$(plist_get ':JVMClassPath')
+	if [[ $JVMClassPath_RAW == *Array* ]] ; then
+		JVMClassPath=.$(plist_get ':JVMClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
+		# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
+		JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	elif [[ ! -z ${JVMClassPath_RAW} ]] ; then
+		JVMClassPath=${JVMClassPath_RAW}
+		# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
+		JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	else
+		#default: fallback to OracleJavaFolder
+		JVMClassPath="${JavaFolder}/*"
+		# Do NOT expand the default 'AppName.app/Contents/Java/*' classpath (#42)
+	fi
+
+	# read the JVM Default Options
+	JVMDefaultOptions=$(plist_get ':JVMDefaultOptions' | grep -o " \-.*" | tr -d '\n' | xargs)
+
+	# read the Main Arguments from JVMArguments key as an array and retain spaces (see #46 for naming details)
+	IFS=$'\t\n'
+	MainArgs=($(xargs -n1 <<<$(plist_get ':JVMArguments' | tr -d '\n' | sed -E 's/Array \{ *(.*) *\}/\1/g' | sed 's/  */ /g')))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the Java version we want to find
+	JVMVersion=$(plist_get ':JVMVersion' | xargs)
+	# post processing of the version string follows below...
+fi
+
+
+
+# JVMVersion: post processing and optional splitting
+if [[ ${JVMVersion} == *";"* ]]; then
+	minMaxArray=(${JVMVersion//;/ })
+	JVMVersion=${minMaxArray[0]//+}
+	JVMMaxVersion=${minMaxArray[1]//+}
+fi
+stub_logger "[JavaRequirement] JVM minimum version: ${JVMVersion}"
+stub_logger "[JavaRequirement] JVM maximum version: ${JVMMaxVersion}"
+
+# MainArgs: replace occurences of $APP_ROOT with its content
+MainArgsArr=()
+for i in "${MainArgs[@]}"
+do
+	MainArgsArr+=("$(eval echo "$i")")
+done
+
+# JVMOptions: replace occurences of $APP_ROOT with its content
+JVMOptionsArr=()
+for i in "${JVMOptions[@]}"
+do
+	JVMOptionsArr+=("$(eval echo "$i")")
+done
+
+
+# internationalized messages
+############################################
+
+LANG=$(defaults read -g AppleLocale)
+stub_logger "[Language] $LANG"
+
+# French localization
+if [[ $LANG == fr* ]] ; then
+	MSG_ERROR_LAUNCHING="ERREUR au lancement de '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="'MainClass' n'est pas spécifié.\nL'application Java ne peut pas être lancée."
+	MSG_JVMVERSION_REQ_INVALID="La syntaxe de la version Java demandée est invalide: %s\nVeuillez contacter le développeur de l'application."
+	MSG_NO_SUITABLE_JAVA="La version de Java installée sur votre système ne convient pas.\nCe programme nécessite Java %s"
+	MSG_JAVA_VERSION_OR_LATER="ou ultérieur"
+	MSG_JAVA_VERSION_LATEST="(dernière mise à jour)"
+	MSG_JAVA_VERSION_MAX="à %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Merci de bien vouloir installer la version de Java requise."
+	MSG_INSTALL_JAVA="Java doit être installé sur votre système.\nRendez-vous sur java.com et suivez les instructions d'installation..."
+	MSG_LATER="Plus tard"
+	MSG_VISIT_JAVA_DOT_COM="Visiter java.com"
+
+# German localization
+elif [[ $LANG == de* ]] ; then
+	MSG_ERROR_LAUNCHING="FEHLER beim Starten von '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="Die 'MainClass' ist nicht spezifiziert!\nDie Java-Anwendung kann nicht gestartet werden!"
+	MSG_JVMVERSION_REQ_INVALID="Die Syntax der angeforderten Java-Version ist ungültig: %s\nBitte kontaktieren Sie den Entwickler der App."
+	MSG_NO_SUITABLE_JAVA="Es wurde keine passende Java-Version auf Ihrem System gefunden!\nDieses Programm benötigt Java %s"
+	MSG_JAVA_VERSION_OR_LATER="oder neuer"
+	MSG_JAVA_VERSION_LATEST="(neuste Unterversion)"
+	MSG_JAVA_VERSION_MAX="bis %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Stellen Sie sicher, dass die angeforderte Java-Version installiert ist."
+	MSG_INSTALL_JAVA="Auf Ihrem System muss die 'Java'-Software installiert sein.\nBesuchen Sie java.com für weitere Installationshinweise."
+	MSG_LATER="Später"
+	MSG_VISIT_JAVA_DOT_COM="java.com öffnen"
+
+# Simplifyed Chinese localization
+elif [[ $LANG == zh* ]] ; then
+	MSG_ERROR_LAUNCHING="无法启动 '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="没有指定 'MainClass'！\nJava程序无法启动!"
+	MSG_JVMVERSION_REQ_INVALID="Java版本参数语法错误: %s\n请联系该应用的开发者。"
+	MSG_NO_SUITABLE_JAVA="没有在系统中找到合适的Java版本！\n必须安装Java %s才能够使用该程序！"
+	MSG_JAVA_VERSION_OR_LATER="及以上版本"
+	MSG_JAVA_VERSION_LATEST="（最新版本）"
+	MSG_JAVA_VERSION_MAX="最高为 %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="请确保系统中安装了所需的Java版本"
+	MSG_INSTALL_JAVA="你需要在Mac中安装Java运行环境！\n访问 java.com 了解如何安装。"
+	MSG_LATER="稍后"
+	MSG_VISIT_JAVA_DOT_COM="访问 java.com"
+
+# English default localization
+else
+	MSG_ERROR_LAUNCHING="ERROR launching '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="'MainClass' isn't specified!\nJava application cannot be started!"
+	MSG_JVMVERSION_REQ_INVALID="The syntax of the required Java version is invalid: %s\nPlease contact the App developer."
+	MSG_NO_SUITABLE_JAVA="No suitable Java version found on your system!\nThis program requires Java %s"
+	MSG_JAVA_VERSION_OR_LATER="or later"
+	MSG_JAVA_VERSION_LATEST="(latest update)"
+	MSG_JAVA_VERSION_MAX="up to %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Make sure you install the required Java version."
+	MSG_INSTALL_JAVA="You need to have JAVA installed on your Mac!\nVisit java.com for installation instructions..."
+	MSG_LATER="Later"
+	MSG_VISIT_JAVA_DOT_COM="Visit java.com"
+fi
+
+
+
+# function 'get_java_version_from_cmd()'
+#
+# returns Java version string from 'java -version' command
+# works for both old (1.8) and new (9) version schema
+#
+# @param1  path to a java JVM executable
+# @return  the Java version number as displayed in 'java -version' command
+################################################################################
+function get_java_version_from_cmd() {
+	# second sed command strips " and -ea from the version string
+	echo $("$1" -version 2>&1 | awk '/version/{print $3}' | sed -E 's/"//g;s/-ea//g')
+}
+
+
+# function 'extract_java_major_version()'
+#
+# extract Java major version from a version string
+#
+# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
+# @return  the major version (e.g. '7', '8' or '9', etc.)
+################################################################################
+function extract_java_major_version() {
+	echo $(echo "$1" | sed -E 's/^1\.//;s/^([0-9]+)(-ea|(\.[0-9_.]{1,7})?)(-b[0-9]+-[0-9]+)?[+*]?$/\1/')
+}
+
+
+# function 'get_comparable_java_version()'
+#
+# return comparable version for a Java version number or requirement string
+#
+# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
+# @return  an 8 digit numeral ('1.8.0_45'->'08000045'; '9.1.13'->'09001013')
+################################################################################
+function get_comparable_java_version() {
+	# cleaning: 1) remove leading '1.'; 2) remove build string (e.g. '-b14-468'); 3) remove 'a-Z' and '-*+' (e.g. '-ea'); 4) replace '_' with '.'
+	local cleaned=$(echo "$1" | sed -E 's/^1\.//g;s/-b[0-9]+-[0-9]+$//g;s/[a-zA-Z+*\-]//g;s/_/./g')
+	# splitting at '.' into an array
+	local arr=( ${cleaned//./ } )
+	# echo a string with left padded version numbers
+	echo "$(printf '%02s' ${arr[0]})$(printf '%03s' ${arr[1]})$(printf '%03s' ${arr[2]})"
+}
+
+
+# function 'is_valid_requirement_pattern()'
+#
+# check whether the Java requirement is a valid requirement pattern
+#
+# supported requirements are for example:
+# - 1.6       requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6*      requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6+      requires Java 6 or higher         [1.6, 1.6.0_45, 1.8, 9, etc.]
+# - 1.6.0     requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6.0_45  requires Java 6u45                [1.6.0_45]
+# - 1.6.0_45+ requires Java 6u45 or higher      [1.6.0_45, 1.6.0_88, 1.8, etc.]
+# - 9         requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
+# - 9*        requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
+# - 9+        requires Java 9 or higher         [9.0, 9.1, 10, etc.]
+# - 9.1       requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
+# - 9.1*      requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
+# - 9.1+      requires Java 9.1 or higher       [9.1, 9.2, 10, etc.]
+# - 9.1.3     requires Java 9.1.3               [9.1.3]
+# - 9.1.3*    requires Java 9.1.3 (any update)  [9.1.3]
+# - 9.1.3+    requires Java 9.1.3 or higher     [9.1.3, 9.1.4, 9.2.*, 10, etc.]
+# - 10-ea     requires Java 10 (early access release)
+#
+# unsupported requirement patterns are for example:
+# - 1.2, 1.3, 1.9       Java 2, 3 are not supported
+# - 1.9                 Java 9 introduced a new versioning scheme
+# - 6u45                known versioning syntax, but unsupported
+# - 9-ea*, 9-ea+        early access releases paired with */+
+# - 9., 9.*, 9.+        version ending with a .
+# - 9.1., 9.1.*, 9.1.+  version ending with a .
+# - 9.3.5.6             4 part version number is unsupported
+#
+# @param1  a Java requirement string ('1.8+')
+# @return  boolean exit code: 0 (is valid), 1 (is not valid)
+################################################################################
+function is_valid_requirement_pattern() {
+	local java_req=$1
+	java8pattern='1\.[4-8](\.0)?(\.0_[0-9]+)?[*+]?'
+	java9pattern='(9|1[0-9])(-ea|[*+]|(\.[0-9]+){1,2}[*+]?)?'
+	# test matches either old Java versioning scheme (up to 1.8) or new scheme (starting with 9)
+	if [[ ${java_req} =~ ^(${java8pattern}|${java9pattern})$ ]]; then
+		return 0
+	else
+		return 1
+	fi
+}
+
+
+
+# determine which JVM to use
+############################################
+
+# default Apple JRE plugin path (< 1.6)
+apple_jre_plugin="/Library/Java/Home/bin/java"
+apple_jre_version=$(get_java_version_from_cmd "${apple_jre_plugin}")
+# default Oracle JRE plugin path (>= 1.7)
+oracle_jre_plugin="/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java"
+oracle_jre_version=$(get_java_version_from_cmd "${oracle_jre_plugin}")
+
+
+# first check system variable "$JAVA_HOME" -> has precedence over any other System JVM
+stub_logger '[JavaSearch] Checking for $JAVA_HOME ...'
+if [ -n "$JAVA_HOME" ] ; then
+	stub_logger "[JavaSearch] ... found JAVA_HOME with value $JAVA_HOME"
+
+	# PR 26: Allow specifying "$JAVA_HOME" relative to "$AppPackageFolder"
+	# which allows for bundling a custom version of Java inside your app!
+	if [[ $JAVA_HOME == /* ]] ; then
+		# if "$JAVA_HOME" starts with a Slash it's an absolute path
+		JAVACMD="$JAVA_HOME/bin/java"
+	else
+		# otherwise it's a relative path to "$AppPackageFolder"
+		JAVACMD="$AppPackageFolder/$JAVA_HOME/bin/java"
+	fi
+	JAVACMD_version=$(get_comparable_java_version $(get_java_version_from_cmd "${JAVACMD}"))
+else
+	stub_logger "[JavaSearch] ... didn't found JAVA_HOME"
+fi
+
+
+# check for any other or a specific Java version
+# also if $JAVA_HOME exists but isn't executable
+if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then
+	stub_logger "[JavaSearch] Checking for JavaVirtualMachines on the system ..."
+	# reset variables
+	JAVACMD=""
+	JAVACMD_version=""
+
+	# first check whether JVMVersion string is a valid requirement string
+	if [ ! -z "${JVMVersion}" ] && ! is_valid_requirement_pattern ${JVMVersion} ; then
+		MSG_JVMVERSION_REQ_INVALID_EXPANDED=$(printf "${MSG_JVMVERSION_REQ_INVALID}" "${JVMVersion}")
+		# log exit cause
+		stub_logger "[EXIT 4] ${MSG_JVMVERSION_REQ_INVALID_EXPANDED}"
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_JVMVERSION_REQ_INVALID_EXPANDED}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
+		# exit with error
+		exit 4
+	fi
+	# then check whether JVMMaxVersion string is a valid requirement string
+	if [ ! -z "${JVMMaxVersion}" ] && ! is_valid_requirement_pattern ${JVMMaxVersion} ; then
+		MSG_JVMVERSION_REQ_INVALID_EXPANDED=$(printf "${MSG_JVMVERSION_REQ_INVALID}" "${JVMMaxVersion}")
+		# log exit cause
+		stub_logger "[EXIT 5] ${MSG_JVMVERSION_REQ_INVALID_EXPANDED}"
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_JVMVERSION_REQ_INVALID_EXPANDED}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
+		# exit with error
+		exit 5
+	fi
+
+
+	# find installed JavaVirtualMachines (JDK + JRE)
+	allJVMs=()
+	# read JDK's from '/usr/libexec/java_home -V' command
+	while read -r line; do
+		version=$(echo $line | awk -F $',' '{print $1;}')
+		path=$(echo $line | awk -F $'" ' '{print $2;}')
+		path+="/bin/java"
+		allJVMs+=("$version:$path")
+	done < <(/usr/libexec/java_home -V 2>&1 | grep '^[[:space:]]')
+	# unset while loop variables
+	unset version path
+
+	# add Apple JRE if available
+	if [ -x "${apple_jre_plugin}" ] ; then
+		allJVMs+=("$apple_jre_version:$apple_jre_plugin")
+	fi
+
+	# add Oracle JRE if available
+	if [ -x "${oracle_jre_plugin}" ] ; then
+		allJVMs+=("$oracle_jre_version:$oracle_jre_plugin")
+	fi
+
+	# debug output
+	for i in "${allJVMs[@]}"
+	do
+		stub_logger "[JavaSearch] ... found JVM: $i"
+	done
+
+
+	# determine JVMs matching the min/max version requirement
+	minC=$(get_comparable_java_version ${JVMVersion})
+	maxC=$(get_comparable_java_version ${JVMMaxVersion})
+	matchingJVMs=()
+
+	for i in "${allJVMs[@]}"
+	do
+		# split JVM string at ':' delimiter to retain spaces in $path substring
+		IFS=: arr=($i) ; unset IFS
+		# [0] JVM version number
+		ver=${arr[0]}
+		# comparable JVM version number
+		comp=$(get_comparable_java_version $ver)
+		# [1] JVM path
+		path="${arr[1]}"
+		# construct string item for adding to the "matchingJVMs" array
+		item="$comp:$ver:$path"
+
+		# pre-requisite: current version number needs to be greater than min version number
+		if [ "$comp" -ge "$minC" ] ; then
+
+			# perform max version checks if max version requirement is present
+			if [ ! -z ${JVMMaxVersion} ] ; then
+
+				# max version requirement ends with '*' modifier
+				if [[ ${JVMMaxVersion} == *\* ]] ; then
+
+					# use the '*' modifier from the max version string as wildcard for a 'starts with' comparison
+					# and check whether the current version number starts with the max version wildcard string
+					if [[ ${ver} == ${JVMMaxVersion} ]]; then
+						matchingJVMs+=("$item")
+
+					# or whether the current comparable version is lower than the comparable max version
+					elif [ "$comp" -le "$maxC" ] ; then
+						matchingJVMs+=("$item")
+					fi
+
+				# max version requirement ends with '+' modifier -> always add this version if it's greater than $min
+				# because a max requirement with + modifier doesn't make sense
+				elif [[ ${JVMMaxVersion} == *+ ]] ; then
+					matchingJVMs+=("$item")
+
+				# matches 6 zeros at the end of the max version string (e.g. for 1.8, 9)
+				# -> then the max version string should be treated like with a '*' modifier at the end
+				#elif [[ ${maxC} =~ ^[0-9]{2}0{6}$ ]] && [ "$comp" -le $(( ${maxC#0} + 999 )) ] ; then
+				#	matchingJVMs+=("$item")
+
+				# matches 3 zeros at the end of the max version string (e.g. for 9.1, 10.3)
+				# -> then the max version string should be treated like with a '*' modifier at the end
+				#elif [[ ${maxC} =~ ^[0-9]{5}0{3}$ ]] && [ "$comp" -le "${maxC}" ] ; then
+				#	matchingJVMs+=("$item")
+
+				# matches standard requirements without modifier
+				elif [ "$comp" -le "$maxC" ]; then
+					matchingJVMs+=("$item")
+				fi
+
+			# no max version requirement:
+
+			# min version requirement ends with '+' modifier
+			# -> always add the current version because it's greater than $min
+			elif [[ ${JVMVersion} == *+ ]] ; then
+				matchingJVMs+=("$item")
+
+			# min version requirement ends with '*' modifier
+			# -> use the '*' modifier from the min version string as wildcard for a 'starts with' comparison
+			#    and check whether the current version number starts with the min version wildcard string
+			elif [[ ${JVMVersion} == *\* ]] ; then
+				if [[ ${ver} == ${JVMVersion} ]] ; then
+					matchingJVMs+=("$item")
+				fi
+
+			# compare the min version against the current version with an additional * wildcard for a 'starts with' comparison
+			# -> e.g. add 1.8.0_44 when the requirement is 1.8
+			elif [[ ${ver} == ${JVMVersion}* ]] ; then
+					matchingJVMs+=("$item")
+			fi
+		fi
+	done
+	# unset for loop variables
+	unset arr ver comp path item
+
+	# debug output
+	for i in "${matchingJVMs[@]}"
+	do
+		stub_logger "[JavaSearch] ... ... matches all requirements: $i"
+	done
+
+
+	# sort the matching JavaVirtualMachines by version number
+	# https://stackoverflow.com/a/11789688/1128689
+	IFS=$'\n' matchingJVMs=($(sort -nr <<<"${matchingJVMs[*]}"))
+	unset IFS
+
+
+	# get the highest matching JVM
+	for ((i = 0; i < ${#matchingJVMs[@]}; i++));
+	do
+		# split JVM string at ':' delimiter to retain spaces in $path substring
+		IFS=: arr=(${matchingJVMs[$i]}) ; unset IFS
+		# [0] comparable JVM version number
+		comp=${arr[0]}
+		# [1] JVM version number
+		ver=${arr[1]}
+		# [2] JVM path
+		path="${arr[2]}"
+
+		# use current value as JAVACMD if it's executable
+		if [ -x "$path" ] ; then
+			JAVACMD="$path"
+			JAVACMD_version=$comp
+			break
+		fi
+	done
+	# unset for loop variables
+	unset arr comp ver path
+fi
+
+# log the Java Command and the extracted version number
+stub_logger "[JavaCommand] '$JAVACMD'"
+stub_logger "[JavaVersion] $(get_java_version_from_cmd "${JAVACMD}")${JAVACMD_version:+ / $JAVACMD_version}"
+
+
+
+if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then
+
+	# different error messages when a specific JVM was required
+	if [ ! -z "${JVMVersion}" ] ; then
+		# display human readable java version (#28)
+		java_version_hr=$(echo ${JVMVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+/ ${MSG_JAVA_VERSION_OR_LATER}/;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
+		MSG_NO_SUITABLE_JAVA_EXPANDED=$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}").
+
+		if [ ! -z "${JVMMaxVersion}" ] ; then
+			java_version_hr=$(extract_java_major_version ${JVMVersion})
+			java_version_max_hr=$(echo ${JVMMaxVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+//;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
+			MSG_NO_SUITABLE_JAVA_EXPANDED="$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}") $(printf "${MSG_JAVA_VERSION_MAX}" "${java_version_max_hr}")"
+		fi
+
+		# log exit cause
+		stub_logger "[EXIT 3] ${MSG_NO_SUITABLE_JAVA_EXPANDED}"
+
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_NO_SUITABLE_JAVA_EXPANDED}\n${MSG_NO_SUITABLE_JAVA_CHECK}\" with title \"${CFBundleName}\"  buttons {\" OK \", \"${MSG_VISIT_JAVA_DOT_COM}\"} default button \"${MSG_VISIT_JAVA_DOT_COM}\" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" \
+				-e "set response to button returned of the result" \
+				-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"http://java.com\""
+		# exit with error
+		exit 3
+
+	else
+		# log exit cause
+		stub_logger "[EXIT 1] ${MSG_ERROR_LAUNCHING}"
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_INSTALL_JAVA}\" with title \"${CFBundleName}\" buttons {\"${MSG_LATER}\", \"${MSG_VISIT_JAVA_DOT_COM}\"} default button \"${MSG_VISIT_JAVA_DOT_COM}\" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" \
+					-e "set response to button returned of the result" \
+					-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"http://java.com\""
+		# exit with error
+		exit 1
+	fi
+fi
+
+
+
+# MainClass check
+############################################
+
+if [ -z "${JVMMainClass}" ]; then
+	# log exit cause
+	stub_logger "[EXIT 2] ${MSG_MISSING_MAINCLASS}"
+	# display error message with AppleScript
+	osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_MISSING_MAINCLASS}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
+	# exit with error
+	exit 2
+fi
+
+
+
+# execute $JAVACMD and do some preparation
+############################################
+
+# enable drag&drop to the dock icon
+export CFProcessPath="$0"
+
+# remove Apples ProcessSerialNumber from passthru arguments (#39)
+if [[ "$*" == -psn* ]] ; then
+	ArgsPassthru=()
+else
+	ArgsPassthru=("$@")
+fi
+
+# change to Working Directory based upon Apple/Oracle Plist info
+cd "${WorkingDirectory}" || exit 13
+stub_logger "[WorkingDirectory] ${WorkingDirectory}"
+
+# execute Java and set
+# - classpath
+# - splash image
+# - dock icon
+# - app name
+# - JVM options / properties (-D)
+# - JVM default options (-X)
+# - main class
+# - main class arguments
+# - passthrough arguments from Terminal or Drag'n'Drop to Finder icon
+stub_logger "[Exec] \"$JAVACMD\" -cp \"${JVMClassPath}\" -splash:\"${ResourcesFolder}/${JVMSplashFile}\" -Xdock:icon=\"${ResourcesFolder}/${CFBundleIconFile}\" -Xdock:name=\"${CFBundleName}\" ${JVMOptionsArr:+$(printf "'%s' " "${JVMOptionsArr[@]}") }${JVMDefaultOptions:+$JVMDefaultOptions }${JVMMainClass}${MainArgsArr:+ $(printf "'%s' " "${MainArgsArr[@]}")}${ArgsPassthru:+ $(printf "'%s' " "${ArgsPassthru[@]}")}"
+exec "${JAVACMD}" \
+		-cp "${JVMClassPath}" \
+		-splash:"${ResourcesFolder}/${JVMSplashFile}" \
+		-Xdock:icon="${ResourcesFolder}/${CFBundleIconFile}" \
+		-Xdock:name="${CFBundleName}" \
+		${JVMOptions:+"${JVMOptions[@]}" }\
+		${JVMDefaultOptions:+$JVMDefaultOptions }\
+		"${JVMMainClass}"\
+		${MainArgsArr:+ "${MainArgsArr[@]}"}\
+		${ArgsPassthru:+ "${ArgsPassthru[@]}"}
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Mac/stub/3-2-0/universalJavaApplicationJREStub beast2-mcmc-2.6.7+dfsg/release/Mac/stub/3-2-0/universalJavaApplicationJREStub
--- beast2-mcmc-2.6.6+dfsg/release/Mac/stub/3-2-0/universalJavaApplicationJREStub	1970-01-01 00:00:00.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Mac/stub/3-2-0/universalJavaApplicationJREStub	2022-04-04 07:18:36.000000000 +0000
@@ -0,0 +1,650 @@
+#!/bin/bash
+##################################################################################
+#                                                                                #
+# universalJavaApplicationStub                                                   #
+#                                                                                #
+# A BASH based JavaApplicationStub for Java Apps on Mac OS X                     #
+# that works with both Apple's and Oracle's plist format.                        #
+#                                                                                #
+# Inspired by Ian Roberts stackoverflow answer                                   #
+# at http://stackoverflow.com/a/17546508/1128689                                 #
+#                                                                                #
+# @author    Tobias Fischer                                                      #
+# @url       https://github.com/tofi86/universalJavaApplicationStub              #
+# @date      2021-02-21                                                          #
+# @version   3.2.0                                                               #
+#                                                                                #
+##################################################################################
+#                                                                                #
+# The MIT License (MIT)                                                          #
+#                                                                                #
+# Copyright (c) 2014-2021 Tobias Fischer                                         #
+#                                                                                #
+# Permission is hereby granted, free of charge, to any person obtaining a copy   #
+# of this software and associated documentation files (the "Software"), to deal  #
+# in the Software without restriction, including without limitation the rights   #
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell      #
+# copies of the Software, and to permit persons to whom the Software is          #
+# furnished to do so, subject to the following conditions:                       #
+#                                                                                #
+# The above copyright notice and this permission notice shall be included in all #
+# copies or substantial portions of the Software.                                #
+#                                                                                #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR     #
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,       #
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE    #
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER         #
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  #
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE  #
+# SOFTWARE.                                                                      #
+#                                                                                #
+##################################################################################
+
+
+
+# function 'stub_logger()'
+#
+# A logger which logs to the macOS Console.app using the 'syslog' command
+#
+# @param1  the log message
+# @return  void
+################################################################################
+function stub_logger() {
+	syslog -s -k \
+		Facility com.apple.console \
+		Level Notice \
+		Sender "$(basename "$0")" \
+		Message "[$$][${CFBundleName:-$(basename "$0")}] $1"
+}
+
+
+
+# set the directory abspath of the current
+# shell script with symlinks being resolved
+############################################
+
+PRG=$0
+while [ -h "$PRG" ]; do
+	ls=$(ls -ld "$PRG")
+	link=$(expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null)
+	if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+		PRG="$link"
+	else
+		PRG="$(dirname "$PRG")/$link"
+	fi
+done
+PROGDIR=$(dirname "$PRG")
+stub_logger "[StubDir] $PROGDIR"
+
+
+
+# set files and folders
+############################################
+
+# the absolute path of the app package
+cd "$PROGDIR"/../../ || exit 11
+AppPackageFolder=$(pwd)
+
+# the base path of the app package
+cd .. || exit 12
+AppPackageRoot=$(pwd)
+
+# set Apple's Java folder
+AppleJavaFolder="${AppPackageFolder}"/Contents/Resources/Java
+
+# set Apple's Resources folder
+AppleResourcesFolder="${AppPackageFolder}"/Contents/Resources
+
+# set Oracle's Java folder
+OracleJavaFolder="${AppPackageFolder}"/Contents/Java
+
+# set Oracle's Resources folder
+OracleResourcesFolder="${AppPackageFolder}"/Contents/Resources
+
+# set path to Info.plist in bundle
+InfoPlistFile="${AppPackageFolder}"/Contents/Info.plist
+
+# set the default JVM Version to a null string
+JVMVersion=""
+JVMMaxVersion=""
+
+
+
+# function 'plist_get()'
+#
+# read a specific Plist key with 'PlistBuddy' utility
+#
+# @param1  the Plist key with leading colon ':'
+# @return  the value as String or Array
+################################################################################
+plist_get(){
+	/usr/libexec/PlistBuddy -c "print $1" "${InfoPlistFile}" 2> /dev/null
+}
+
+# function 'plist_get_java()'
+#
+# read a specific Plist key with 'PlistBuddy' utility
+# in the 'Java' or 'JavaX' dictionary (<dict>)
+#
+# @param1  the Plist :Java(X):Key with leading colon ':'
+# @return  the value as String or Array
+################################################################################
+plist_get_java(){
+	plist_get ${JavaKey:-":Java"}$1
+}
+
+
+
+# read Info.plist and extract JVM options
+############################################
+
+# read the program name from CFBundleName
+CFBundleName=$(plist_get ':CFBundleName')
+
+# read the icon file name
+CFBundleIconFile=$(plist_get ':CFBundleIconFile')
+
+
+# check Info.plist for Apple style Java keys -> if key :Java is present, parse in apple mode
+/usr/libexec/PlistBuddy -c "print :Java" "${InfoPlistFile}" > /dev/null 2>&1
+exitcode=$?
+JavaKey=":Java"
+
+# if no :Java key is present, check Info.plist for universalJavaApplication style JavaX keys -> if key :JavaX is present, parse in apple mode
+if [ $exitcode -ne 0 ]; then
+	/usr/libexec/PlistBuddy -c "print :JavaX" "${InfoPlistFile}" > /dev/null 2>&1
+	exitcode=$?
+	JavaKey=":JavaX"
+fi
+
+
+# read 'Info.plist' file in Apple style if exit code returns 0 (true, ':Java' key is present)
+if [ $exitcode -eq 0 ]; then
+	stub_logger "[PlistStyle] Apple"
+
+	# set Java and Resources folder
+	JavaFolder="${AppleJavaFolder}"
+	ResourcesFolder="${AppleResourcesFolder}"
+
+	# set expandable variables
+	APP_ROOT="${AppPackageFolder}"
+	APP_PACKAGE="${AppPackageFolder}"
+	JAVAROOT="${AppleJavaFolder}"
+	USER_HOME="$HOME"
+
+
+	# read the Java WorkingDirectory
+	JVMWorkDir=$(plist_get_java ':WorkingDirectory' | xargs)
+	# set Working Directory based upon PList value
+	if [[ ! -z ${JVMWorkDir} ]]; then
+		WorkingDirectory="${JVMWorkDir}"
+	else
+		# AppPackageRoot is the standard WorkingDirectory when the script is started
+		WorkingDirectory="${AppPackageRoot}"
+	fi
+	# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+	WorkingDirectory=$(eval echo "${WorkingDirectory}")
+
+
+	# read the MainClass name
+	JVMMainClass="$(plist_get_java ':MainClass')"
+
+	# read the SplashFile name
+	JVMSplashFile=$(plist_get_java ':SplashFile')
+
+	# read the JVM Properties as an array and retain spaces
+	IFS=$'\t\n'
+	JVMOptions=($(xargs -n1 <<<$(plist_get_java ':Properties' | grep " =" | sed 's/^ */-D/g' | sed -E 's/ = (.*)$/="\1"/g')))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the ClassPath in either Array or String style
+	JVMClassPath_RAW=$(plist_get_java ':ClassPath' | xargs)
+	if [[ $JVMClassPath_RAW == *Array* ]] ; then
+		JVMClassPath=.$(plist_get_java ':ClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
+	else
+		JVMClassPath=${JVMClassPath_RAW}
+	fi
+	# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+	JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	# read the JVM Options in either Array or String style
+	JVMDefaultOptions_RAW=$(plist_get_java ':VMOptions' | xargs)
+	if [[ $JVMDefaultOptions_RAW == *Array* ]] ; then
+		JVMDefaultOptions=$(plist_get_java ':VMOptions' | grep "    " | sed 's/^ */ /g' | tr -d '\n' | xargs)
+	else
+		JVMDefaultOptions=${JVMDefaultOptions_RAW}
+	fi
+	# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME (#84)
+	JVMDefaultOptions=$(eval echo "${JVMDefaultOptions}")
+
+	# read StartOnMainThread and add as -XstartOnFirstThread
+	JVMStartOnMainThread=$(plist_get_java ':StartOnMainThread')
+	if [ "${JVMStartOnMainThread}" == "true" ]; then
+		JVMDefaultOptions+=" -XstartOnFirstThread"
+	fi
+
+	# read the JVM Arguments in either Array or String style (#76) and retain spaces
+	IFS=$'\t\n'
+	MainArgs_RAW=$(plist_get_java ':Arguments' | xargs)
+	if [[ $MainArgs_RAW == *Array* ]] ; then
+		MainArgs=($(xargs -n1 <<<$(plist_get_java ':Arguments' | tr -d '\n' | sed -E 's/Array \{ *(.*) *\}/\1/g' | sed 's/  */ /g')))
+	else
+		MainArgs=($(xargs -n1 <<<$(plist_get_java ':Arguments')))
+	fi
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the Java version we want to find
+	JVMVersion=$(plist_get_java ':JVMVersion' | xargs)
+	# post processing of the version string follows below...
+
+
+# read 'Info.plist' file in Oracle style
+else
+	stub_logger "[PlistStyle] Oracle"
+
+	# set Working Directory and Java and Resources folder
+	JavaFolder="${OracleJavaFolder}"
+	ResourcesFolder="${OracleResourcesFolder}"
+	WorkingDirectory="${OracleJavaFolder}"
+
+	# set expandable variables
+	APP_ROOT="${AppPackageFolder}"
+	APP_PACKAGE="${AppPackageFolder}"
+	JAVAROOT="${OracleJavaFolder}"
+	USER_HOME="$HOME"
+
+	# read the MainClass name
+	JVMMainClass="$(plist_get ':JVMMainClassName')"
+
+	# read the SplashFile name
+	JVMSplashFile=$(plist_get ':JVMSplashFile')
+
+	# read the JVM Options as an array and retain spaces
+	IFS=$'\t\n'
+	JVMOptions=($(plist_get ':JVMOptions' | grep "    " | sed 's/^ *//g'))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the ClassPath in either Array or String style
+	JVMClassPath_RAW=$(plist_get ':JVMClassPath')
+	if [[ $JVMClassPath_RAW == *Array* ]] ; then
+		JVMClassPath=.$(plist_get ':JVMClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
+		# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+		JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	elif [[ ! -z ${JVMClassPath_RAW} ]] ; then
+		JVMClassPath=${JVMClassPath_RAW}
+		# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+		JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	else
+		#default: fallback to OracleJavaFolder
+		JVMClassPath="${JavaFolder}/*"
+		# Do NOT expand the default 'AppName.app/Contents/Java/*' classpath (#42)
+	fi
+
+	# read the JVM Default Options by parsing the :JVMDefaultOptions <dict>
+	# and pulling all <string> values starting with a dash (-)
+	JVMDefaultOptions=$(plist_get ':JVMDefaultOptions' | grep -o " \-.*" | tr -d '\n' | xargs)
+	# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME (#99)
+	JVMDefaultOptions=$(eval echo "${JVMDefaultOptions}")
+
+	# read the Main Arguments from JVMArguments key as an array and retain spaces (see #46 for naming details)
+	IFS=$'\t\n'
+	MainArgs=($(xargs -n1 <<<$(plist_get ':JVMArguments' | tr -d '\n' | sed -E 's/Array \{ *(.*) *\}/\1/g' | sed 's/  */ /g')))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the Java version we want to find
+	JVMVersion=$(plist_get ':JVMVersion' | xargs)
+	# post processing of the version string follows below...
+fi
+
+
+# (#75) check for undefined icons or icon names without .icns extension and prepare
+# an osascript statement for those cases when the icon can be shown in the dialog
+DialogWithIcon=""
+if [ ! -z ${CFBundleIconFile} ]; then
+	if [[ ${CFBundleIconFile} == *.icns ]] && [[ -f "${ResourcesFolder}/${CFBundleIconFile}" ]] ; then
+		DialogWithIcon=" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
+	elif [[ ${CFBundleIconFile} != *.icns ]] && [[ -f "${ResourcesFolder}/${CFBundleIconFile}.icns" ]] ; then
+		CFBundleIconFile+=".icns"
+		DialogWithIcon=" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
+	fi
+fi
+
+
+# JVMVersion: post processing and optional splitting
+if [[ ${JVMVersion} == *";"* ]]; then
+	minMaxArray=(${JVMVersion//;/ })
+	JVMVersion=${minMaxArray[0]//+}
+	JVMMaxVersion=${minMaxArray[1]//+}
+fi
+stub_logger "[JavaRequirement] JVM minimum version: ${JVMVersion}"
+stub_logger "[JavaRequirement] JVM maximum version: ${JVMMaxVersion}"
+
+# MainArgs: expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+MainArgsArr=()
+for i in "${MainArgs[@]}"
+do
+	MainArgsArr+=("$(eval echo "$i")")
+done
+
+# JVMOptions: expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+JVMOptionsArr=()
+for i in "${JVMOptions[@]}"
+do
+	JVMOptionsArr+=("$(eval echo "$i")")
+done
+
+
+# internationalized messages
+############################################
+
+# supported languages / available translations
+stubLanguages="^(fr|de|zh|es|en)-"
+
+# read user preferred languages as defined in macOS System Preferences (#101)
+stub_logger '[LanguageSearch] Checking preferred languages in macOS System Preferences...'
+appleLanguages=($(defaults read -g AppleLanguages | grep '\s"' | tr -d ',' | xargs))
+stub_logger "[LanguageSearch] ... found [${appleLanguages[*]}]"
+
+language=""
+for i in "${appleLanguages[@]}"
+do
+	langValue="${i%-*}"
+    if [[ "$i" =~ $stubLanguages ]]; then 
+		stub_logger "[LanguageSearch] ... selected '$i' ('$langValue') as the default language for the launcher stub"
+		language=${langValue}
+        break
+	fi
+done
+if [ -z "${language}" ]; then
+    language="en"
+    stub_logger "[LanguageSearch] ... selected fallback 'en' as the default language for the launcher stub"
+fi
+stub_logger "[Language] $language"
+
+
+case "${language}" in
+# French
+fr)
+	MSG_ERROR_LAUNCHING="ERREUR au lancement de '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="'MainClass' n'est pas spécifié.\nL'application Java ne peut pas être lancée."
+	MSG_JVMVERSION_REQ_INVALID="La syntaxe de la version de Java demandée est invalide: %s\nVeuillez contacter le développeur de l'application."
+	MSG_NO_SUITABLE_JAVA="La version de Java installée sur votre système ne convient pas.\nCe programme nécessite Java %s"
+	MSG_JAVA_VERSION_OR_LATER="ou ultérieur"
+	MSG_JAVA_VERSION_LATEST="(dernière mise à jour)"
+	MSG_JAVA_VERSION_MAX="à %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Merci de bien vouloir installer la version de Java requise."
+	MSG_INSTALL_JAVA="Java doit être installé sur votre système.\nRendez-vous sur java.com et suivez les instructions d'installation..."
+	MSG_LATER="Plus tard"
+	MSG_VISIT_JAVA_DOT_COM="Java by Oracle"
+	MSG_VISIT_ADOPTOPENJDK="Java by AdoptOpenJDK"
+    ;;
+
+# German
+de)
+	MSG_ERROR_LAUNCHING="FEHLER beim Starten von '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="Die 'MainClass' ist nicht spezifiziert!\nDie Java-Anwendung kann nicht gestartet werden!"
+	MSG_JVMVERSION_REQ_INVALID="Die Syntax der angeforderten Java-Version ist ungültig: %s\nBitte kontaktieren Sie den Entwickler der App."
+	MSG_NO_SUITABLE_JAVA="Es wurde keine passende Java-Version auf Ihrem System gefunden!\nDieses Programm benötigt Java %s"
+	MSG_JAVA_VERSION_OR_LATER="oder neuer"
+	MSG_JAVA_VERSION_LATEST="(neuste Unterversion)"
+	MSG_JAVA_VERSION_MAX="bis %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Stellen Sie sicher, dass die angeforderte Java-Version installiert ist."
+	MSG_INSTALL_JAVA="Auf Ihrem System muss die 'Java'-Software installiert sein.\nBesuchen Sie java.com für weitere Installationshinweise."
+	MSG_LATER="Später"
+	MSG_VISIT_JAVA_DOT_COM="Java von Oracle"
+	MSG_VISIT_ADOPTOPENJDK="Java von AdoptOpenJDK"
+    ;;
+
+# Simplified Chinese
+zh)
+	MSG_ERROR_LAUNCHING="无法启动 '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="没有指定 'MainClass'！\nJava程序无法启动!"
+	MSG_JVMVERSION_REQ_INVALID="Java版本参数语法错误: %s\n请联系该应用的开发者。"
+	MSG_NO_SUITABLE_JAVA="没有在系统中找到合适的Java版本！\n必须安装Java %s才能够使用该程序！"
+	MSG_JAVA_VERSION_OR_LATER="及以上版本"
+	MSG_JAVA_VERSION_LATEST="（最新版本）"
+	MSG_JAVA_VERSION_MAX="最高为 %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="请确保系统中安装了所需的Java版本"
+	MSG_INSTALL_JAVA="你需要在Mac中安装Java运行环境！\n访问 java.com 了解如何安装。"
+	MSG_LATER="稍后"
+	MSG_VISIT_JAVA_DOT_COM="Java by Oracle"
+	MSG_VISIT_ADOPTOPENJDK="Java by AdoptOpenJDK"
+    ;;
+
+# Spanish
+es)
+	MSG_ERROR_LAUNCHING="ERROR iniciando '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="¡'MainClass' no especificada!\n¡La aplicación Java no puede iniciarse!"
+	MSG_JVMVERSION_REQ_INVALID="La sintaxis de la versión Java requerida no es válida: %s\nPor favor, contacte con el desarrollador de la aplicación."
+	MSG_NO_SUITABLE_JAVA="¡No se encontró una versión de Java adecuada en su sistema!\nEste programa requiere Java %s"
+	MSG_JAVA_VERSION_OR_LATER="o posterior"
+	MSG_JAVA_VERSION_LATEST="(ultima actualización)"
+	MSG_JAVA_VERSION_MAX="superior a %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Asegúrese de instalar la versión Java requerida."
+	MSG_INSTALL_JAVA="¡Necesita tener JAVA instalado en su Mac!\nVisite java.com para consultar las instrucciones para su instalación..."
+	MSG_LATER="Más tarde"
+	MSG_VISIT_JAVA_DOT_COM="Java de Oracle"
+	MSG_VISIT_ADOPTOPENJDK="Java de AdoptOpenJDK"
+    ;;
+
+# English | default
+en|*)
+	MSG_ERROR_LAUNCHING="ERROR launching '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="'MainClass' isn't specified!\nJava application cannot be started!"
+	MSG_JVMVERSION_REQ_INVALID="The syntax of the required Java version is invalid: %s\nPlease contact the App developer."
+	MSG_NO_SUITABLE_JAVA="No suitable Java version found on your system!\nThis program requires Java %s"
+	MSG_JAVA_VERSION_OR_LATER="or later"
+	MSG_JAVA_VERSION_LATEST="(latest update)"
+	MSG_JAVA_VERSION_MAX="up to %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Make sure you install the required Java version."
+	MSG_INSTALL_JAVA="You need to have JAVA installed on your Mac!\nVisit java.com for installation instructions..."
+	MSG_LATER="Later"
+	MSG_VISIT_JAVA_DOT_COM="Java by Oracle"
+	MSG_VISIT_ADOPTOPENJDK="Java by AdoptOpenJDK"
+    ;;
+esac
+
+
+
+# function 'get_java_version_from_cmd()'
+#
+# returns Java version string from 'java -version' command
+# works for both old (1.8) and new (9) version schema
+#
+# @param1  path to a java JVM executable
+# @return  the Java version number as displayed in 'java -version' command
+################################################################################
+function get_java_version_from_cmd() {
+	# second sed command strips " and -ea from the version string
+	echo $("$1" -version 2>&1 | awk '/version/{print $3}' | sed -E 's/"//g;s/-ea//g')
+}
+
+
+# function 'extract_java_major_version()'
+#
+# extract Java major version from a version string
+#
+# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
+# @return  the major version (e.g. '7', '8' or '9', etc.)
+################################################################################
+function extract_java_major_version() {
+	echo $(echo "$1" | sed -E 's/^1\.//;s/^([0-9]+)(-ea|(\.[0-9_.]{1,7})?)(-b[0-9]+-[0-9]+)?[+*]?$/\1/')
+}
+
+
+# function 'get_comparable_java_version()'
+#
+# return comparable version for a Java version number or requirement string
+#
+# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
+# @return  an 8 digit numeral ('1.8.0_45'->'08000045'; '9.1.13'->'09001013')
+################################################################################
+function get_comparable_java_version() {
+	# cleaning: 1) remove leading '1.'; 2) remove build string (e.g. '-b14-468'); 3) remove 'a-Z' and '-*+' (e.g. '-ea'); 4) replace '_' with '.'
+	local cleaned=$(echo "$1" | sed -E 's/^1\.//g;s/-b[0-9]+-[0-9]+$//g;s/[a-zA-Z+*\-]//g;s/_/./g')
+	# splitting at '.' into an array
+	local arr=( ${cleaned//./ } )
+	# echo a string with left padded version numbers
+	echo "$(printf '%02s' ${arr[0]})$(printf '%03s' ${arr[1]})$(printf '%03s' ${arr[2]})"
+}
+
+
+# function 'is_valid_requirement_pattern()'
+#
+# check whether the Java requirement is a valid requirement pattern
+#
+# supported requirements are for example:
+# - 1.6       requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6*      requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6+      requires Java 6 or higher         [1.6, 1.6.0_45, 1.8, 9, etc.]
+# - 1.6.0     requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6.0_45  requires Java 6u45                [1.6.0_45]
+# - 1.6.0_45+ requires Java 6u45 or higher      [1.6.0_45, 1.6.0_88, 1.8, etc.]
+# - 9         requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
+# - 9*        requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
+# - 9+        requires Java 9 or higher         [9.0, 9.1, 10, etc.]
+# - 9.1       requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
+# - 9.1*      requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
+# - 9.1+      requires Java 9.1 or higher       [9.1, 9.2, 10, etc.]
+# - 9.1.3     requires Java 9.1.3               [9.1.3]
+# - 9.1.3*    requires Java 9.1.3 (any update)  [9.1.3]
+# - 9.1.3+    requires Java 9.1.3 or higher     [9.1.3, 9.1.4, 9.2.*, 10, etc.]
+# - 10-ea     requires Java 10 (early access release)
+#
+# unsupported requirement patterns are for example:
+# - 1.2, 1.3, 1.9       Java 2, 3 are not supported
+# - 1.9                 Java 9 introduced a new versioning scheme
+# - 6u45                known versioning syntax, but unsupported
+# - 9-ea*, 9-ea+        early access releases paired with */+
+# - 9., 9.*, 9.+        version ending with a .
+# - 9.1., 9.1.*, 9.1.+  version ending with a .
+# - 9.3.5.6             4 part version number is unsupported
+#
+# @param1  a Java requirement string ('1.8+')
+# @return  boolean exit code: 0 (is valid), 1 (is not valid)
+################################################################################
+function is_valid_requirement_pattern() {
+	local java_req=$1
+	java8pattern='1\.[4-8](\.[0-9]+)?(\.0_[0-9]+)?[*+]?'
+	java9pattern='(9|1[0-9])(-ea|[*+]|(\.[0-9]+){1,2}[*+]?)?'
+	# test matches either old Java versioning scheme (up to 1.8) or new scheme (starting with 9)
+	if [[ ${java_req} =~ ^(${java8pattern}|${java9pattern})$ ]]; then
+		return 0
+	else
+		return 1
+	fi
+}
+
+
+
+# determine which JVM to use
+############################################
+
+# modified for BEAST 2 with JRE
+JAVACMD="${AppPackageFolder}/../jre1.8.0_292/bin/java"
+
+
+# log the Java Command and the extracted version number
+stub_logger "[JavaCommand] '$JAVACMD'"
+stub_logger "[JavaVersion] $(get_java_version_from_cmd "${JAVACMD}")${JAVACMD_version:+ / $JAVACMD_version}"
+
+
+
+if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then
+
+	# different error messages when a specific JVM was required
+	if [ ! -z "${JVMVersion}" ] ; then
+		# display human readable java version (#28)
+		java_version_hr=$(echo ${JVMVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+/ ${MSG_JAVA_VERSION_OR_LATER}/;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
+		MSG_NO_SUITABLE_JAVA_EXPANDED=$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}").
+
+		if [ ! -z "${JVMMaxVersion}" ] ; then
+			java_version_hr=$(extract_java_major_version ${JVMVersion})
+			java_version_max_hr=$(echo ${JVMMaxVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+//;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
+			MSG_NO_SUITABLE_JAVA_EXPANDED="$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}") $(printf "${MSG_JAVA_VERSION_MAX}" "${java_version_max_hr}")"
+		fi
+
+		# log exit cause
+		stub_logger "[EXIT 3] ${MSG_NO_SUITABLE_JAVA_EXPANDED}"
+
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_NO_SUITABLE_JAVA_EXPANDED}\n${MSG_NO_SUITABLE_JAVA_CHECK}\" with title \"${CFBundleName}\"  buttons {\" OK \", \"${MSG_VISIT_JAVA_DOT_COM}\", \"${MSG_VISIT_ADOPTOPENJDK}\"} default button 1${DialogWithIcon}" \
+				-e "set response to button returned of the result" \
+				-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"https://www.java.com/download/\"" \
+				-e "if response is \"${MSG_VISIT_ADOPTOPENJDK}\" then open location \"https://adoptopenjdk.net/releases.html\""
+		# exit with error
+		exit 3
+
+	else
+		# log exit cause
+		stub_logger "[EXIT 1] ${MSG_ERROR_LAUNCHING}"
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_INSTALL_JAVA}\" with title \"${CFBundleName}\" buttons {\"${MSG_LATER}\", \"${MSG_VISIT_JAVA_DOT_COM}\", \"${MSG_VISIT_ADOPTOPENJDK}\"} default button 1${DialogWithIcon}" \
+					-e "set response to button returned of the result" \
+					-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"https://www.java.com/download/\"" \
+					-e "if response is \"${MSG_VISIT_ADOPTOPENJDK}\" then open location \"https://adoptopenjdk.net/releases.html\""
+		# exit with error
+		exit 1
+	fi
+fi
+
+
+
+# MainClass check
+############################################
+
+if [ -z "${JVMMainClass}" ]; then
+	# log exit cause
+	stub_logger "[EXIT 2] ${MSG_MISSING_MAINCLASS}"
+	# display error message with AppleScript
+	osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_MISSING_MAINCLASS}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1${DialogWithIcon}"
+	# exit with error
+	exit 2
+fi
+
+
+
+# execute $JAVACMD and do some preparation
+############################################
+
+# enable drag&drop to the dock icon
+export CFProcessPath="$0"
+
+# remove Apples ProcessSerialNumber from passthru arguments (#39)
+if [[ "$*" == -psn* ]] ; then
+	ArgsPassthru=()
+else
+	ArgsPassthru=("$@")
+fi
+
+# change to Working Directory based upon Apple/Oracle Plist info
+cd "${WorkingDirectory}" || exit 13
+stub_logger "[WorkingDirectory] ${WorkingDirectory}"
+
+# execute Java and set
+# - classpath
+# - splash image
+# - dock icon
+# - app name
+# - JVM options / properties (-D)
+# - JVM default options (-X)
+# - main class
+# - main class arguments
+# - passthrough arguments from Terminal or Drag'n'Drop to Finder icon
+stub_logger "[Exec] \"$JAVACMD\" -cp \"${JVMClassPath}\" ${JVMSplashFile:+ -splash:\"${ResourcesFolder}/${JVMSplashFile}\"} -Xdock:icon=\"${ResourcesFolder}/${CFBundleIconFile}\" -Xdock:name=\"${CFBundleName}\" ${JVMOptionsArr:+$(printf "'%s' " "${JVMOptionsArr[@]}") }${JVMDefaultOptions:+$JVMDefaultOptions }${JVMMainClass}${MainArgsArr:+ $(printf "'%s' " "${MainArgsArr[@]}")}${ArgsPassthru:+ $(printf "'%s' " "${ArgsPassthru[@]}")}"
+exec "${JAVACMD}" \
+		-cp "${JVMClassPath}" \
+		${JVMSplashFile:+ -splash:"${ResourcesFolder}/${JVMSplashFile}"} \
+		-Xdock:icon="${ResourcesFolder}/${CFBundleIconFile}" \
+		-Xdock:name="${CFBundleName}" \
+		${JVMOptionsArr:+"${JVMOptionsArr[@]}" }\
+		${JVMDefaultOptions:+$JVMDefaultOptions }\
+		"${JVMMainClass}"\
+		${MainArgsArr:+ "${MainArgsArr[@]}"}\
+		${ArgsPassthru:+ "${ArgsPassthru[@]}"}
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Mac/stub/3-2-0/universalJavaApplicationStub beast2-mcmc-2.6.7+dfsg/release/Mac/stub/3-2-0/universalJavaApplicationStub
--- beast2-mcmc-2.6.6+dfsg/release/Mac/stub/3-2-0/universalJavaApplicationStub	1970-01-01 00:00:00.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Mac/stub/3-2-0/universalJavaApplicationStub	2022-04-04 07:18:36.000000000 +0000
@@ -0,0 +1,888 @@
+#!/bin/bash
+##################################################################################
+#                                                                                #
+# universalJavaApplicationStub                                                   #
+#                                                                                #
+# A BASH based JavaApplicationStub for Java Apps on Mac OS X                     #
+# that works with both Apple's and Oracle's plist format.                        #
+#                                                                                #
+# Inspired by Ian Roberts stackoverflow answer                                   #
+# at http://stackoverflow.com/a/17546508/1128689                                 #
+#                                                                                #
+# @author    Tobias Fischer                                                      #
+# @url       https://github.com/tofi86/universalJavaApplicationStub              #
+# @date      2021-02-21                                                          #
+# @version   3.2.0                                                               #
+#                                                                                #
+##################################################################################
+#                                                                                #
+# The MIT License (MIT)                                                          #
+#                                                                                #
+# Copyright (c) 2014-2021 Tobias Fischer                                         #
+#                                                                                #
+# Permission is hereby granted, free of charge, to any person obtaining a copy   #
+# of this software and associated documentation files (the "Software"), to deal  #
+# in the Software without restriction, including without limitation the rights   #
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell      #
+# copies of the Software, and to permit persons to whom the Software is          #
+# furnished to do so, subject to the following conditions:                       #
+#                                                                                #
+# The above copyright notice and this permission notice shall be included in all #
+# copies or substantial portions of the Software.                                #
+#                                                                                #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR     #
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,       #
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE    #
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER         #
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  #
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE  #
+# SOFTWARE.                                                                      #
+#                                                                                #
+##################################################################################
+
+
+
+# function 'stub_logger()'
+#
+# A logger which logs to the macOS Console.app using the 'syslog' command
+#
+# @param1  the log message
+# @return  void
+################################################################################
+function stub_logger() {
+	syslog -s -k \
+		Facility com.apple.console \
+		Level Notice \
+		Sender "$(basename "$0")" \
+		Message "[$$][${CFBundleName:-$(basename "$0")}] $1"
+}
+
+
+
+# set the directory abspath of the current
+# shell script with symlinks being resolved
+############################################
+
+PRG=$0
+while [ -h "$PRG" ]; do
+	ls=$(ls -ld "$PRG")
+	link=$(expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null)
+	if expr "$link" : '^/' 2> /dev/null >/dev/null; then
+		PRG="$link"
+	else
+		PRG="$(dirname "$PRG")/$link"
+	fi
+done
+PROGDIR=$(dirname "$PRG")
+stub_logger "[StubDir] $PROGDIR"
+
+
+
+# set files and folders
+############################################
+
+# the absolute path of the app package
+cd "$PROGDIR"/../../ || exit 11
+AppPackageFolder=$(pwd)
+
+# the base path of the app package
+cd .. || exit 12
+AppPackageRoot=$(pwd)
+
+# set Apple's Java folder
+AppleJavaFolder="${AppPackageFolder}"/Contents/Resources/Java
+
+# set Apple's Resources folder
+AppleResourcesFolder="${AppPackageFolder}"/Contents/Resources
+
+# set Oracle's Java folder
+OracleJavaFolder="${AppPackageFolder}"/Contents/Java
+
+# set Oracle's Resources folder
+OracleResourcesFolder="${AppPackageFolder}"/Contents/Resources
+
+# set path to Info.plist in bundle
+InfoPlistFile="${AppPackageFolder}"/Contents/Info.plist
+
+# set the default JVM Version to a null string
+JVMVersion=""
+JVMMaxVersion=""
+
+
+
+# function 'plist_get()'
+#
+# read a specific Plist key with 'PlistBuddy' utility
+#
+# @param1  the Plist key with leading colon ':'
+# @return  the value as String or Array
+################################################################################
+plist_get(){
+	/usr/libexec/PlistBuddy -c "print $1" "${InfoPlistFile}" 2> /dev/null
+}
+
+# function 'plist_get_java()'
+#
+# read a specific Plist key with 'PlistBuddy' utility
+# in the 'Java' or 'JavaX' dictionary (<dict>)
+#
+# @param1  the Plist :Java(X):Key with leading colon ':'
+# @return  the value as String or Array
+################################################################################
+plist_get_java(){
+	plist_get ${JavaKey:-":Java"}$1
+}
+
+
+
+# read Info.plist and extract JVM options
+############################################
+
+# read the program name from CFBundleName
+CFBundleName=$(plist_get ':CFBundleName')
+
+# read the icon file name
+CFBundleIconFile=$(plist_get ':CFBundleIconFile')
+
+
+# check Info.plist for Apple style Java keys -> if key :Java is present, parse in apple mode
+/usr/libexec/PlistBuddy -c "print :Java" "${InfoPlistFile}" > /dev/null 2>&1
+exitcode=$?
+JavaKey=":Java"
+
+# if no :Java key is present, check Info.plist for universalJavaApplication style JavaX keys -> if key :JavaX is present, parse in apple mode
+if [ $exitcode -ne 0 ]; then
+	/usr/libexec/PlistBuddy -c "print :JavaX" "${InfoPlistFile}" > /dev/null 2>&1
+	exitcode=$?
+	JavaKey=":JavaX"
+fi
+
+
+# read 'Info.plist' file in Apple style if exit code returns 0 (true, ':Java' key is present)
+if [ $exitcode -eq 0 ]; then
+	stub_logger "[PlistStyle] Apple"
+
+	# set Java and Resources folder
+	JavaFolder="${AppleJavaFolder}"
+	ResourcesFolder="${AppleResourcesFolder}"
+
+	# set expandable variables
+	APP_ROOT="${AppPackageFolder}"
+	APP_PACKAGE="${AppPackageFolder}"
+	JAVAROOT="${AppleJavaFolder}"
+	USER_HOME="$HOME"
+
+
+	# read the Java WorkingDirectory
+	JVMWorkDir=$(plist_get_java ':WorkingDirectory' | xargs)
+	# set Working Directory based upon PList value
+	if [[ ! -z ${JVMWorkDir} ]]; then
+		WorkingDirectory="${JVMWorkDir}"
+	else
+		# AppPackageRoot is the standard WorkingDirectory when the script is started
+		WorkingDirectory="${AppPackageRoot}"
+	fi
+	# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+	WorkingDirectory=$(eval echo "${WorkingDirectory}")
+
+
+	# read the MainClass name
+	JVMMainClass="$(plist_get_java ':MainClass')"
+
+	# read the SplashFile name
+	JVMSplashFile=$(plist_get_java ':SplashFile')
+
+	# read the JVM Properties as an array and retain spaces
+	IFS=$'\t\n'
+	JVMOptions=($(xargs -n1 <<<$(plist_get_java ':Properties' | grep " =" | sed 's/^ */-D/g' | sed -E 's/ = (.*)$/="\1"/g')))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the ClassPath in either Array or String style
+	JVMClassPath_RAW=$(plist_get_java ':ClassPath' | xargs)
+	if [[ $JVMClassPath_RAW == *Array* ]] ; then
+		JVMClassPath=.$(plist_get_java ':ClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
+	else
+		JVMClassPath=${JVMClassPath_RAW}
+	fi
+	# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+	JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	# read the JVM Options in either Array or String style
+	JVMDefaultOptions_RAW=$(plist_get_java ':VMOptions' | xargs)
+	if [[ $JVMDefaultOptions_RAW == *Array* ]] ; then
+		JVMDefaultOptions=$(plist_get_java ':VMOptions' | grep "    " | sed 's/^ */ /g' | tr -d '\n' | xargs)
+	else
+		JVMDefaultOptions=${JVMDefaultOptions_RAW}
+	fi
+	# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME (#84)
+	JVMDefaultOptions=$(eval echo "${JVMDefaultOptions}")
+
+	# read StartOnMainThread and add as -XstartOnFirstThread
+	JVMStartOnMainThread=$(plist_get_java ':StartOnMainThread')
+	if [ "${JVMStartOnMainThread}" == "true" ]; then
+		JVMDefaultOptions+=" -XstartOnFirstThread"
+	fi
+
+	# read the JVM Arguments in either Array or String style (#76) and retain spaces
+	IFS=$'\t\n'
+	MainArgs_RAW=$(plist_get_java ':Arguments' | xargs)
+	if [[ $MainArgs_RAW == *Array* ]] ; then
+		MainArgs=($(xargs -n1 <<<$(plist_get_java ':Arguments' | tr -d '\n' | sed -E 's/Array \{ *(.*) *\}/\1/g' | sed 's/  */ /g')))
+	else
+		MainArgs=($(xargs -n1 <<<$(plist_get_java ':Arguments')))
+	fi
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the Java version we want to find
+	JVMVersion=$(plist_get_java ':JVMVersion' | xargs)
+	# post processing of the version string follows below...
+
+
+# read 'Info.plist' file in Oracle style
+else
+	stub_logger "[PlistStyle] Oracle"
+
+	# set Working Directory and Java and Resources folder
+	JavaFolder="${OracleJavaFolder}"
+	ResourcesFolder="${OracleResourcesFolder}"
+	WorkingDirectory="${OracleJavaFolder}"
+
+	# set expandable variables
+	APP_ROOT="${AppPackageFolder}"
+	APP_PACKAGE="${AppPackageFolder}"
+	JAVAROOT="${OracleJavaFolder}"
+	USER_HOME="$HOME"
+
+	# read the MainClass name
+	JVMMainClass="$(plist_get ':JVMMainClassName')"
+
+	# read the SplashFile name
+	JVMSplashFile=$(plist_get ':JVMSplashFile')
+
+	# read the JVM Options as an array and retain spaces
+	IFS=$'\t\n'
+	JVMOptions=($(plist_get ':JVMOptions' | grep "    " | sed 's/^ *//g'))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the ClassPath in either Array or String style
+	JVMClassPath_RAW=$(plist_get ':JVMClassPath')
+	if [[ $JVMClassPath_RAW == *Array* ]] ; then
+		JVMClassPath=.$(plist_get ':JVMClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
+		# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+		JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	elif [[ ! -z ${JVMClassPath_RAW} ]] ; then
+		JVMClassPath=${JVMClassPath_RAW}
+		# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+		JVMClassPath=$(eval echo "${JVMClassPath}")
+
+	else
+		#default: fallback to OracleJavaFolder
+		JVMClassPath="${JavaFolder}/*"
+		# Do NOT expand the default 'AppName.app/Contents/Java/*' classpath (#42)
+	fi
+
+	# read the JVM Default Options by parsing the :JVMDefaultOptions <dict>
+	# and pulling all <string> values starting with a dash (-)
+	JVMDefaultOptions=$(plist_get ':JVMDefaultOptions' | grep -o " \-.*" | tr -d '\n' | xargs)
+	# expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME (#99)
+	JVMDefaultOptions=$(eval echo "${JVMDefaultOptions}")
+
+	# read the Main Arguments from JVMArguments key as an array and retain spaces (see #46 for naming details)
+	IFS=$'\t\n'
+	MainArgs=($(xargs -n1 <<<$(plist_get ':JVMArguments' | tr -d '\n' | sed -E 's/Array \{ *(.*) *\}/\1/g' | sed 's/  */ /g')))
+	unset IFS
+	# post processing of the array follows further below...
+
+	# read the Java version we want to find
+	JVMVersion=$(plist_get ':JVMVersion' | xargs)
+	# post processing of the version string follows below...
+fi
+
+
+# (#75) check for undefined icons or icon names without .icns extension and prepare
+# an osascript statement for those cases when the icon can be shown in the dialog
+DialogWithIcon=""
+if [ ! -z ${CFBundleIconFile} ]; then
+	if [[ ${CFBundleIconFile} == *.icns ]] && [[ -f "${ResourcesFolder}/${CFBundleIconFile}" ]] ; then
+		DialogWithIcon=" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
+	elif [[ ${CFBundleIconFile} != *.icns ]] && [[ -f "${ResourcesFolder}/${CFBundleIconFile}.icns" ]] ; then
+		CFBundleIconFile+=".icns"
+		DialogWithIcon=" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
+	fi
+fi
+
+
+# JVMVersion: post processing and optional splitting
+if [[ ${JVMVersion} == *";"* ]]; then
+	minMaxArray=(${JVMVersion//;/ })
+	JVMVersion=${minMaxArray[0]//+}
+	JVMMaxVersion=${minMaxArray[1]//+}
+fi
+stub_logger "[JavaRequirement] JVM minimum version: ${JVMVersion}"
+stub_logger "[JavaRequirement] JVM maximum version: ${JVMMaxVersion}"
+
+# MainArgs: expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+MainArgsArr=()
+for i in "${MainArgs[@]}"
+do
+	MainArgsArr+=("$(eval echo "$i")")
+done
+
+# JVMOptions: expand variables $APP_PACKAGE, $APP_ROOT, $JAVAROOT, $USER_HOME
+JVMOptionsArr=()
+for i in "${JVMOptions[@]}"
+do
+	JVMOptionsArr+=("$(eval echo "$i")")
+done
+
+
+# internationalized messages
+############################################
+
+# supported languages / available translations
+stubLanguages="^(fr|de|zh|es|en)-"
+
+# read user preferred languages as defined in macOS System Preferences (#101)
+stub_logger '[LanguageSearch] Checking preferred languages in macOS System Preferences...'
+appleLanguages=($(defaults read -g AppleLanguages | grep '\s"' | tr -d ',' | xargs))
+stub_logger "[LanguageSearch] ... found [${appleLanguages[*]}]"
+
+language=""
+for i in "${appleLanguages[@]}"
+do
+	langValue="${i%-*}"
+    if [[ "$i" =~ $stubLanguages ]]; then 
+		stub_logger "[LanguageSearch] ... selected '$i' ('$langValue') as the default language for the launcher stub"
+		language=${langValue}
+        break
+	fi
+done
+if [ -z "${language}" ]; then
+    language="en"
+    stub_logger "[LanguageSearch] ... selected fallback 'en' as the default language for the launcher stub"
+fi
+stub_logger "[Language] $language"
+
+
+case "${language}" in
+# French
+fr)
+	MSG_ERROR_LAUNCHING="ERREUR au lancement de '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="'MainClass' n'est pas spécifié.\nL'application Java ne peut pas être lancée."
+	MSG_JVMVERSION_REQ_INVALID="La syntaxe de la version de Java demandée est invalide: %s\nVeuillez contacter le développeur de l'application."
+	MSG_NO_SUITABLE_JAVA="La version de Java installée sur votre système ne convient pas.\nCe programme nécessite Java %s"
+	MSG_JAVA_VERSION_OR_LATER="ou ultérieur"
+	MSG_JAVA_VERSION_LATEST="(dernière mise à jour)"
+	MSG_JAVA_VERSION_MAX="à %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Merci de bien vouloir installer la version de Java requise."
+	MSG_INSTALL_JAVA="Java doit être installé sur votre système.\nRendez-vous sur java.com et suivez les instructions d'installation..."
+	MSG_LATER="Plus tard"
+	MSG_VISIT_JAVA_DOT_COM="Java by Oracle"
+	MSG_VISIT_ADOPTOPENJDK="Java by AdoptOpenJDK"
+    ;;
+
+# German
+de)
+	MSG_ERROR_LAUNCHING="FEHLER beim Starten von '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="Die 'MainClass' ist nicht spezifiziert!\nDie Java-Anwendung kann nicht gestartet werden!"
+	MSG_JVMVERSION_REQ_INVALID="Die Syntax der angeforderten Java-Version ist ungültig: %s\nBitte kontaktieren Sie den Entwickler der App."
+	MSG_NO_SUITABLE_JAVA="Es wurde keine passende Java-Version auf Ihrem System gefunden!\nDieses Programm benötigt Java %s"
+	MSG_JAVA_VERSION_OR_LATER="oder neuer"
+	MSG_JAVA_VERSION_LATEST="(neuste Unterversion)"
+	MSG_JAVA_VERSION_MAX="bis %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Stellen Sie sicher, dass die angeforderte Java-Version installiert ist."
+	MSG_INSTALL_JAVA="Auf Ihrem System muss die 'Java'-Software installiert sein.\nBesuchen Sie java.com für weitere Installationshinweise."
+	MSG_LATER="Später"
+	MSG_VISIT_JAVA_DOT_COM="Java von Oracle"
+	MSG_VISIT_ADOPTOPENJDK="Java von AdoptOpenJDK"
+    ;;
+
+# Simplified Chinese
+zh)
+	MSG_ERROR_LAUNCHING="无法启动 '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="没有指定 'MainClass'！\nJava程序无法启动!"
+	MSG_JVMVERSION_REQ_INVALID="Java版本参数语法错误: %s\n请联系该应用的开发者。"
+	MSG_NO_SUITABLE_JAVA="没有在系统中找到合适的Java版本！\n必须安装Java %s才能够使用该程序！"
+	MSG_JAVA_VERSION_OR_LATER="及以上版本"
+	MSG_JAVA_VERSION_LATEST="（最新版本）"
+	MSG_JAVA_VERSION_MAX="最高为 %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="请确保系统中安装了所需的Java版本"
+	MSG_INSTALL_JAVA="你需要在Mac中安装Java运行环境！\n访问 java.com 了解如何安装。"
+	MSG_LATER="稍后"
+	MSG_VISIT_JAVA_DOT_COM="Java by Oracle"
+	MSG_VISIT_ADOPTOPENJDK="Java by AdoptOpenJDK"
+    ;;
+
+# Spanish
+es)
+	MSG_ERROR_LAUNCHING="ERROR iniciando '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="¡'MainClass' no especificada!\n¡La aplicación Java no puede iniciarse!"
+	MSG_JVMVERSION_REQ_INVALID="La sintaxis de la versión Java requerida no es válida: %s\nPor favor, contacte con el desarrollador de la aplicación."
+	MSG_NO_SUITABLE_JAVA="¡No se encontró una versión de Java adecuada en su sistema!\nEste programa requiere Java %s"
+	MSG_JAVA_VERSION_OR_LATER="o posterior"
+	MSG_JAVA_VERSION_LATEST="(ultima actualización)"
+	MSG_JAVA_VERSION_MAX="superior a %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Asegúrese de instalar la versión Java requerida."
+	MSG_INSTALL_JAVA="¡Necesita tener JAVA instalado en su Mac!\nVisite java.com para consultar las instrucciones para su instalación..."
+	MSG_LATER="Más tarde"
+	MSG_VISIT_JAVA_DOT_COM="Java de Oracle"
+	MSG_VISIT_ADOPTOPENJDK="Java de AdoptOpenJDK"
+    ;;
+
+# English | default
+en|*)
+	MSG_ERROR_LAUNCHING="ERROR launching '${CFBundleName}'."
+	MSG_MISSING_MAINCLASS="'MainClass' isn't specified!\nJava application cannot be started!"
+	MSG_JVMVERSION_REQ_INVALID="The syntax of the required Java version is invalid: %s\nPlease contact the App developer."
+	MSG_NO_SUITABLE_JAVA="No suitable Java version found on your system!\nThis program requires Java %s"
+	MSG_JAVA_VERSION_OR_LATER="or later"
+	MSG_JAVA_VERSION_LATEST="(latest update)"
+	MSG_JAVA_VERSION_MAX="up to %s"
+	MSG_NO_SUITABLE_JAVA_CHECK="Make sure you install the required Java version."
+	MSG_INSTALL_JAVA="You need to have JAVA installed on your Mac!\nVisit java.com for installation instructions..."
+	MSG_LATER="Later"
+	MSG_VISIT_JAVA_DOT_COM="Java by Oracle"
+	MSG_VISIT_ADOPTOPENJDK="Java by AdoptOpenJDK"
+    ;;
+esac
+
+
+
+# function 'get_java_version_from_cmd()'
+#
+# returns Java version string from 'java -version' command
+# works for both old (1.8) and new (9) version schema
+#
+# @param1  path to a java JVM executable
+# @return  the Java version number as displayed in 'java -version' command
+################################################################################
+function get_java_version_from_cmd() {
+	# second sed command strips " and -ea from the version string
+	echo $("$1" -version 2>&1 | awk '/version/{print $3}' | sed -E 's/"//g;s/-ea//g')
+}
+
+
+# function 'extract_java_major_version()'
+#
+# extract Java major version from a version string
+#
+# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
+# @return  the major version (e.g. '7', '8' or '9', etc.)
+################################################################################
+function extract_java_major_version() {
+	echo $(echo "$1" | sed -E 's/^1\.//;s/^([0-9]+)(-ea|(\.[0-9_.]{1,7})?)(-b[0-9]+-[0-9]+)?[+*]?$/\1/')
+}
+
+
+# function 'get_comparable_java_version()'
+#
+# return comparable version for a Java version number or requirement string
+#
+# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
+# @return  an 8 digit numeral ('1.8.0_45'->'08000045'; '9.1.13'->'09001013')
+################################################################################
+function get_comparable_java_version() {
+	# cleaning: 1) remove leading '1.'; 2) remove build string (e.g. '-b14-468'); 3) remove 'a-Z' and '-*+' (e.g. '-ea'); 4) replace '_' with '.'
+	local cleaned=$(echo "$1" | sed -E 's/^1\.//g;s/-b[0-9]+-[0-9]+$//g;s/[a-zA-Z+*\-]//g;s/_/./g')
+	# splitting at '.' into an array
+	local arr=( ${cleaned//./ } )
+	# echo a string with left padded version numbers
+	echo "$(printf '%02s' ${arr[0]})$(printf '%03s' ${arr[1]})$(printf '%03s' ${arr[2]})"
+}
+
+
+# function 'is_valid_requirement_pattern()'
+#
+# check whether the Java requirement is a valid requirement pattern
+#
+# supported requirements are for example:
+# - 1.6       requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6*      requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6+      requires Java 6 or higher         [1.6, 1.6.0_45, 1.8, 9, etc.]
+# - 1.6.0     requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
+# - 1.6.0_45  requires Java 6u45                [1.6.0_45]
+# - 1.6.0_45+ requires Java 6u45 or higher      [1.6.0_45, 1.6.0_88, 1.8, etc.]
+# - 9         requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
+# - 9*        requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
+# - 9+        requires Java 9 or higher         [9.0, 9.1, 10, etc.]
+# - 9.1       requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
+# - 9.1*      requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
+# - 9.1+      requires Java 9.1 or higher       [9.1, 9.2, 10, etc.]
+# - 9.1.3     requires Java 9.1.3               [9.1.3]
+# - 9.1.3*    requires Java 9.1.3 (any update)  [9.1.3]
+# - 9.1.3+    requires Java 9.1.3 or higher     [9.1.3, 9.1.4, 9.2.*, 10, etc.]
+# - 10-ea     requires Java 10 (early access release)
+#
+# unsupported requirement patterns are for example:
+# - 1.2, 1.3, 1.9       Java 2, 3 are not supported
+# - 1.9                 Java 9 introduced a new versioning scheme
+# - 6u45                known versioning syntax, but unsupported
+# - 9-ea*, 9-ea+        early access releases paired with */+
+# - 9., 9.*, 9.+        version ending with a .
+# - 9.1., 9.1.*, 9.1.+  version ending with a .
+# - 9.3.5.6             4 part version number is unsupported
+#
+# @param1  a Java requirement string ('1.8+')
+# @return  boolean exit code: 0 (is valid), 1 (is not valid)
+################################################################################
+function is_valid_requirement_pattern() {
+	local java_req=$1
+	java8pattern='1\.[4-8](\.[0-9]+)?(\.0_[0-9]+)?[*+]?'
+	java9pattern='(9|1[0-9])(-ea|[*+]|(\.[0-9]+){1,2}[*+]?)?'
+	# test matches either old Java versioning scheme (up to 1.8) or new scheme (starting with 9)
+	if [[ ${java_req} =~ ^(${java8pattern}|${java9pattern})$ ]]; then
+		return 0
+	else
+		return 1
+	fi
+}
+
+
+
+# determine which JVM to use
+############################################
+
+# default Apple JRE plugin path (< 1.6)
+apple_jre_plugin="/Library/Java/Home/bin/java"
+apple_jre_version=$(get_java_version_from_cmd "${apple_jre_plugin}")
+# default Oracle JRE plugin path (>= 1.7)
+oracle_jre_plugin="/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java"
+oracle_jre_version=$(get_java_version_from_cmd "${oracle_jre_plugin}")
+
+
+# first check system variable "$JAVA_HOME" -> has precedence over any other System JVM
+stub_logger '[JavaSearch] Checking for $JAVA_HOME ...'
+if [ -n "$JAVA_HOME" ] ; then
+	stub_logger "[JavaSearch] ... found JAVA_HOME with value $JAVA_HOME"
+
+	# PR 26: Allow specifying "$JAVA_HOME" relative to "$AppPackageFolder"
+	# which allows for bundling a custom version of Java inside your app!
+	if [[ $JAVA_HOME == /* ]] ; then
+		# if "$JAVA_HOME" starts with a Slash it's an absolute path
+		JAVACMD="$JAVA_HOME/bin/java"
+		stub_logger "[JavaSearch] ... parsing JAVA_HOME as absolute path to the executable '$JAVACMD'"
+	else
+		# otherwise it's a relative path to "$AppPackageFolder"
+		JAVACMD="$AppPackageFolder/$JAVA_HOME/bin/java"
+		stub_logger "[JavaSearch] ... parsing JAVA_HOME as relative path inside the App bundle to the executable '$JAVACMD'"
+	fi
+	JAVACMD_version=$(get_comparable_java_version $(get_java_version_from_cmd "${JAVACMD}"))
+else
+	stub_logger "[JavaSearch] ... haven't found JAVA_HOME"
+fi
+
+
+# check for any other or a specific Java version
+# also if $JAVA_HOME exists but isn't executable
+if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then
+
+	# add a warning in the syslog if JAVA_HOME is not executable or not found (#100)
+	if [ -n "$JAVA_HOME" ] ; then
+		stub_logger "[JavaSearch] ... but no 'java' executable was found at the JAVA_HOME location!"
+	fi
+
+	stub_logger "[JavaSearch] Searching for JavaVirtualMachines on the system ..."
+	# reset variables
+	JAVACMD=""
+	JAVACMD_version=""
+
+	# first check whether JVMVersion string is a valid requirement string
+	if [ ! -z "${JVMVersion}" ] && ! is_valid_requirement_pattern ${JVMVersion} ; then
+		MSG_JVMVERSION_REQ_INVALID_EXPANDED=$(printf "${MSG_JVMVERSION_REQ_INVALID}" "${JVMVersion}")
+		# log exit cause
+		stub_logger "[EXIT 4] ${MSG_JVMVERSION_REQ_INVALID_EXPANDED}"
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_JVMVERSION_REQ_INVALID_EXPANDED}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1${DialogWithIcon}"
+		# exit with error
+		exit 4
+	fi
+	# then check whether JVMMaxVersion string is a valid requirement string
+	if [ ! -z "${JVMMaxVersion}" ] && ! is_valid_requirement_pattern ${JVMMaxVersion} ; then
+		MSG_JVMVERSION_REQ_INVALID_EXPANDED=$(printf "${MSG_JVMVERSION_REQ_INVALID}" "${JVMMaxVersion}")
+		# log exit cause
+		stub_logger "[EXIT 5] ${MSG_JVMVERSION_REQ_INVALID_EXPANDED}"
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_JVMVERSION_REQ_INVALID_EXPANDED}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1${DialogWithIcon}"
+		# exit with error
+		exit 5
+	fi
+
+
+	# find installed JavaVirtualMachines (JDK + JRE)
+	allJVMs=()
+	
+	# read JDK's from '/usr/libexec/java_home --xml' command with PlistBuddy and a custom Dict iterator
+	# idea: https://stackoverflow.com/a/14085460/1128689 and https://scriptingosx.com/2018/07/parsing-dscl-output-in-scripts/
+	javaXml=$(/usr/libexec/java_home --xml)
+	javaCounter=$(/usr/libexec/PlistBuddy -c "Print" /dev/stdin <<< $javaXml | grep "Dict" | wc -l | tr -d ' ')
+
+	# iterate over all Dict entries
+	# but only if there are any JVMs at all (#93)
+	if [ "$javaCounter" -gt "0" ] ; then
+		for idx in $(seq 0 $((javaCounter - 1)))
+		do
+			version=$(/usr/libexec/PlistBuddy -c "print :$idx:JVMVersion" /dev/stdin <<< $javaXml)
+			path=$(/usr/libexec/PlistBuddy -c "print :$idx:JVMHomePath" /dev/stdin <<< $javaXml)
+			path+="/bin/java"
+			allJVMs+=("$version:$path")
+		done
+		# unset for loop variables
+		unset version path
+	fi
+
+	# add SDKMAN! java versions (#95)
+	if [ -d ~/.sdkman/candidates/java/ ] ; then
+		for sdkjdk in ~/.sdkman/candidates/java/*/
+		do
+			if [[ ${sdkjdk} =~ /current/$ ]] ; then
+				continue
+			fi
+
+			sdkjdkcmd="${sdkjdk}bin/java"
+			version=$(get_java_version_from_cmd "${sdkjdkcmd}")
+			allJVMs+=("$version:$sdkjdkcmd")
+		done
+		# unset for loop variables
+		unset version
+	fi
+
+	# add Apple JRE if available
+	if [ -x "${apple_jre_plugin}" ] ; then
+		allJVMs+=("$apple_jre_version:$apple_jre_plugin")
+	fi
+
+	# add Oracle JRE if available
+	if [ -x "${oracle_jre_plugin}" ] ; then
+		allJVMs+=("$oracle_jre_version:$oracle_jre_plugin")
+	fi
+
+	# debug output
+	for i in "${allJVMs[@]}"
+	do
+		stub_logger "[JavaSearch] ... found JVM: $i"
+	done
+
+
+	# determine JVMs matching the min/max version requirement
+
+	stub_logger "[JavaSearch] Filtering the result list for JVMs matching the min/max version requirement ..."
+
+	minC=$(get_comparable_java_version ${JVMVersion})
+	maxC=$(get_comparable_java_version ${JVMMaxVersion})
+	matchingJVMs=()
+
+	for i in "${allJVMs[@]}"
+	do
+		# split JVM string at ':' delimiter to retain spaces in $path substring
+		IFS=: arr=($i) ; unset IFS
+		# [0] JVM version number
+		ver=${arr[0]}
+		# comparable JVM version number
+		comp=$(get_comparable_java_version $ver)
+		# [1] JVM path
+		path="${arr[1]}"
+		# construct string item for adding to the "matchingJVMs" array
+		item="$comp:$ver:$path"
+
+		# pre-requisite: current version number needs to be greater than min version number
+		if [ "$comp" -ge "$minC" ] ; then
+
+			# perform max version checks if max version requirement is present
+			if [ ! -z ${JVMMaxVersion} ] ; then
+
+				# max version requirement ends with '*' modifier
+				if [[ ${JVMMaxVersion} == *\* ]] ; then
+
+					# use the '*' modifier from the max version string as wildcard for a 'starts with' comparison
+					# and check whether the current version number starts with the max version wildcard string
+					if [[ ${ver} == ${JVMMaxVersion} ]]; then
+						matchingJVMs+=("$item")
+
+					# or whether the current comparable version is lower than the comparable max version
+					elif [ "$comp" -le "$maxC" ] ; then
+						matchingJVMs+=("$item")
+					fi
+
+				# max version requirement ends with '+' modifier -> always add this version if it's greater than $min
+				# because a max requirement with + modifier doesn't make sense
+				elif [[ ${JVMMaxVersion} == *+ ]] ; then
+					matchingJVMs+=("$item")
+
+				# matches 6 zeros at the end of the max version string (e.g. for 1.8, 9)
+				# -> then the max version string should be treated like with a '*' modifier at the end
+				#elif [[ ${maxC} =~ ^[0-9]{2}0{6}$ ]] && [ "$comp" -le $(( ${maxC#0} + 999 )) ] ; then
+				#	matchingJVMs+=("$item")
+
+				# matches 3 zeros at the end of the max version string (e.g. for 9.1, 10.3)
+				# -> then the max version string should be treated like with a '*' modifier at the end
+				#elif [[ ${maxC} =~ ^[0-9]{5}0{3}$ ]] && [ "$comp" -le "${maxC}" ] ; then
+				#	matchingJVMs+=("$item")
+
+				# matches standard requirements without modifier
+				elif [ "$comp" -le "$maxC" ]; then
+					matchingJVMs+=("$item")
+				fi
+
+			# no max version requirement:
+
+			# min version requirement ends with '+' modifier
+			# -> always add the current version because it's greater than $min
+			elif [[ ${JVMVersion} == *+ ]] ; then
+				matchingJVMs+=("$item")
+
+			# min version requirement ends with '*' modifier
+			# -> use the '*' modifier from the min version string as wildcard for a 'starts with' comparison
+			#    and check whether the current version number starts with the min version wildcard string
+			elif [[ ${JVMVersion} == *\* ]] ; then
+				if [[ ${ver} == ${JVMVersion} ]] ; then
+					matchingJVMs+=("$item")
+				fi
+
+			# compare the min version against the current version with an additional * wildcard for a 'starts with' comparison
+			# -> e.g. add 1.8.0_44 when the requirement is 1.8
+			elif [[ ${ver} == ${JVMVersion}* ]] ; then
+					matchingJVMs+=("$item")
+			fi
+		fi
+	done
+	# unset for loop variables
+	unset arr ver comp path item
+
+	# debug output
+	for i in "${matchingJVMs[@]}"
+	do
+		stub_logger "[JavaSearch] ... matches all requirements: $i"
+	done
+
+
+	# sort the matching JavaVirtualMachines by version number
+	# https://stackoverflow.com/a/11789688/1128689
+	IFS=$'\n' matchingJVMs=($(sort -nr <<<"${matchingJVMs[*]}"))
+	unset IFS
+
+
+	# get the highest matching JVM
+	for ((i = 0; i < ${#matchingJVMs[@]}; i++));
+	do
+		# split JVM string at ':' delimiter to retain spaces in $path substring
+		IFS=: arr=(${matchingJVMs[$i]}) ; unset IFS
+		# [0] comparable JVM version number
+		comp=${arr[0]}
+		# [1] JVM version number
+		ver=${arr[1]}
+		# [2] JVM path
+		path="${arr[2]}"
+
+		# use current value as JAVACMD if it's executable
+		if [ -x "$path" ] ; then
+			JAVACMD="$path"
+			JAVACMD_version=$comp
+			break
+		fi
+	done
+	# unset for loop variables
+	unset arr comp ver path
+fi
+
+# log the Java Command and the extracted version number
+stub_logger "[JavaCommand] '$JAVACMD'"
+stub_logger "[JavaVersion] $(get_java_version_from_cmd "${JAVACMD}")${JAVACMD_version:+ / $JAVACMD_version}"
+
+
+
+if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then
+
+	# different error messages when a specific JVM was required
+	if [ ! -z "${JVMVersion}" ] ; then
+		# display human readable java version (#28)
+		java_version_hr=$(echo ${JVMVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+/ ${MSG_JAVA_VERSION_OR_LATER}/;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
+		MSG_NO_SUITABLE_JAVA_EXPANDED=$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}").
+
+		if [ ! -z "${JVMMaxVersion}" ] ; then
+			java_version_hr=$(extract_java_major_version ${JVMVersion})
+			java_version_max_hr=$(echo ${JVMMaxVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+//;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
+			MSG_NO_SUITABLE_JAVA_EXPANDED="$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}") $(printf "${MSG_JAVA_VERSION_MAX}" "${java_version_max_hr}")"
+		fi
+
+		# log exit cause
+		stub_logger "[EXIT 3] ${MSG_NO_SUITABLE_JAVA_EXPANDED}"
+
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_NO_SUITABLE_JAVA_EXPANDED}\n${MSG_NO_SUITABLE_JAVA_CHECK}\" with title \"${CFBundleName}\"  buttons {\" OK \", \"${MSG_VISIT_JAVA_DOT_COM}\", \"${MSG_VISIT_ADOPTOPENJDK}\"} default button 1${DialogWithIcon}" \
+				-e "set response to button returned of the result" \
+				-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"https://www.java.com/download/\"" \
+				-e "if response is \"${MSG_VISIT_ADOPTOPENJDK}\" then open location \"https://adoptopenjdk.net/releases.html\""
+		# exit with error
+		exit 3
+
+	else
+		# log exit cause
+		stub_logger "[EXIT 1] ${MSG_ERROR_LAUNCHING}"
+		# display error message with AppleScript
+		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_INSTALL_JAVA}\" with title \"${CFBundleName}\" buttons {\"${MSG_LATER}\", \"${MSG_VISIT_JAVA_DOT_COM}\", \"${MSG_VISIT_ADOPTOPENJDK}\"} default button 1${DialogWithIcon}" \
+					-e "set response to button returned of the result" \
+					-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"https://www.java.com/download/\"" \
+					-e "if response is \"${MSG_VISIT_ADOPTOPENJDK}\" then open location \"https://adoptopenjdk.net/releases.html\""
+		# exit with error
+		exit 1
+	fi
+fi
+
+
+
+# MainClass check
+############################################
+
+if [ -z "${JVMMainClass}" ]; then
+	# log exit cause
+	stub_logger "[EXIT 2] ${MSG_MISSING_MAINCLASS}"
+	# display error message with AppleScript
+	osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_MISSING_MAINCLASS}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1${DialogWithIcon}"
+	# exit with error
+	exit 2
+fi
+
+
+
+# execute $JAVACMD and do some preparation
+############################################
+
+# enable drag&drop to the dock icon
+export CFProcessPath="$0"
+
+# remove Apples ProcessSerialNumber from passthru arguments (#39)
+if [[ "$*" == -psn* ]] ; then
+	ArgsPassthru=()
+else
+	ArgsPassthru=("$@")
+fi
+
+# change to Working Directory based upon Apple/Oracle Plist info
+cd "${WorkingDirectory}" || exit 13
+stub_logger "[WorkingDirectory] ${WorkingDirectory}"
+
+# execute Java and set
+# - classpath
+# - splash image
+# - dock icon
+# - app name
+# - JVM options / properties (-D)
+# - JVM default options (-X)
+# - main class
+# - main class arguments
+# - passthrough arguments from Terminal or Drag'n'Drop to Finder icon
+stub_logger "[Exec] \"$JAVACMD\" -cp \"${JVMClassPath}\" ${JVMSplashFile:+ -splash:\"${ResourcesFolder}/${JVMSplashFile}\"} -Xdock:icon=\"${ResourcesFolder}/${CFBundleIconFile}\" -Xdock:name=\"${CFBundleName}\" ${JVMOptionsArr:+$(printf "'%s' " "${JVMOptionsArr[@]}") }${JVMDefaultOptions:+$JVMDefaultOptions }${JVMMainClass}${MainArgsArr:+ $(printf "'%s' " "${MainArgsArr[@]}")}${ArgsPassthru:+ $(printf "'%s' " "${ArgsPassthru[@]}")}"
+exec "${JAVACMD}" \
+		-cp "${JVMClassPath}" \
+		${JVMSplashFile:+ -splash:"${ResourcesFolder}/${JVMSplashFile}"} \
+		-Xdock:icon="${ResourcesFolder}/${CFBundleIconFile}" \
+		-Xdock:name="${CFBundleName}" \
+		${JVMOptionsArr:+"${JVMOptionsArr[@]}" }\
+		${JVMDefaultOptions:+$JVMDefaultOptions }\
+		"${JVMMainClass}"\
+		${MainArgsArr:+ "${MainArgsArr[@]}"}\
+		${ArgsPassthru:+ "${ArgsPassthru[@]}"}
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Mac/universalJavaApplicationJREStub beast2-mcmc-2.6.7+dfsg/release/Mac/universalJavaApplicationJREStub
--- beast2-mcmc-2.6.6+dfsg/release/Mac/universalJavaApplicationJREStub	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Mac/universalJavaApplicationJREStub	1970-01-01 00:00:00.000000000 +0000
@@ -1,572 +0,0 @@
-#!/bin/bash
-##################################################################################
-#                                                                                #
-# universalJavaApplicationStub                                                   #
-#                                                                                #
-# A BASH based JavaApplicationStub for Java Apps on Mac OS X                     #
-# that works with both Apple's and Oracle's plist format.                        #
-#                                                                                #
-# Inspired by Ian Roberts stackoverflow answer                                   #
-# at http://stackoverflow.com/a/17546508/1128689                                 #
-#                                                                                #
-# @author    Tobias Fischer                                                      #
-# @url       https://github.com/tofi86/universalJavaApplicationStub              #
-# @date      2018-07-29                                                          #
-# @version   3.0.3                                                               #
-#                                                                                #
-##################################################################################
-#                                                                                #
-# The MIT License (MIT)                                                          #
-#                                                                                #
-# Copyright (c) 2014-2018 Tobias Fischer                                         #
-#                                                                                #
-# Permission is hereby granted, free of charge, to any person obtaining a copy   #
-# of this software and associated documentation files (the "Software"), to deal  #
-# in the Software without restriction, including without limitation the rights   #
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell      #
-# copies of the Software, and to permit persons to whom the Software is          #
-# furnished to do so, subject to the following conditions:                       #
-#                                                                                #
-# The above copyright notice and this permission notice shall be included in all #
-# copies or substantial portions of the Software.                                #
-#                                                                                #
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR     #
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,       #
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE    #
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER         #
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  #
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE  #
-# SOFTWARE.                                                                      #
-#                                                                                #
-##################################################################################
-
-
-
-# function 'stub_logger()'
-#
-# A logger which logs to the macOS Console.app using the 'syslog' command
-#
-# @param1  the log message
-# @return  void
-################################################################################
-function stub_logger() {
-	syslog -s -k \
-		Facility com.apple.console \
-		Level Notice \
-		Sender "$(basename "$0")" \
-		Message "[$$][${CFBundleName:-$(basename "$0")}] $1"
-}
-
-
-
-# set the directory abspath of the current
-# shell script with symlinks being resolved
-############################################
-
-PRG=$0
-while [ -h "$PRG" ]; do
-	ls=$(ls -ld "$PRG")
-	link=$(expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null)
-	if expr "$link" : '^/' 2> /dev/null >/dev/null; then
-		PRG="$link"
-	else
-		PRG="$(dirname "$PRG")/$link"
-	fi
-done
-PROGDIR=$(dirname "$PRG")
-stub_logger "[StubDir] $PROGDIR"
-
-
-
-# set files and folders
-############################################
-
-# the absolute path of the app package
-cd "$PROGDIR"/../../ || exit 11
-AppPackageFolder=$(pwd)
-
-# the base path of the app package
-cd .. || exit 12
-AppPackageRoot=$(pwd)
-
-# set Apple's Java folder
-AppleJavaFolder="${AppPackageFolder}"/Contents/Resources/Java
-
-# set Apple's Resources folder
-AppleResourcesFolder="${AppPackageFolder}"/Contents/Resources
-
-# set Oracle's Java folder
-OracleJavaFolder="${AppPackageFolder}"/Contents/Java
-
-# set Oracle's Resources folder
-OracleResourcesFolder="${AppPackageFolder}"/Contents/Resources
-
-# set path to Info.plist in bundle
-InfoPlistFile="${AppPackageFolder}"/Contents/Info.plist
-
-# set the default JVM Version to a null string
-JVMVersion=""
-JVMMaxVersion=""
-
-
-
-# function 'plist_get()'
-#
-# read a specific Plist key with 'PlistBuddy' utility
-#
-# @param1  the Plist key with leading colon ':'
-# @return  the value as String or Array
-################################################################################
-plist_get(){
-	/usr/libexec/PlistBuddy -c "print $1" "${InfoPlistFile}" 2> /dev/null
-}
-
-# function 'plist_get_java()'
-#
-# read a specific Plist key with 'PlistBuddy' utility
-# in the 'Java' or 'JavaX' dictionary (<dict>)
-#
-# @param1  the Plist :Java(X):Key with leading colon ':'
-# @return  the value as String or Array
-################################################################################
-plist_get_java(){
-	plist_get ${JavaKey:-":Java"}$1
-}
-
-
-
-# read Info.plist and extract JVM options
-############################################
-
-# read the program name from CFBundleName
-CFBundleName=$(plist_get ':CFBundleName')
-
-# read the icon file name
-CFBundleIconFile=$(plist_get ':CFBundleIconFile')
-
-
-# check Info.plist for Apple style Java keys -> if key :Java is present, parse in apple mode
-/usr/libexec/PlistBuddy -c "print :Java" "${InfoPlistFile}" > /dev/null 2>&1
-exitcode=$?
-JavaKey=":Java"
-
-# if no :Java key is present, check Info.plist for universalJavaApplication style JavaX keys -> if key :JavaX is present, parse in apple mode
-if [ $exitcode -ne 0 ]; then
-	/usr/libexec/PlistBuddy -c "print :JavaX" "${InfoPlistFile}" > /dev/null 2>&1
-	exitcode=$?
-	JavaKey=":JavaX"
-fi
-
-
-# read 'Info.plist' file in Apple style if exit code returns 0 (true, ':Java' key is present)
-if [ $exitcode -eq 0 ]; then
-	stub_logger "[PlistStyle] Apple"
-
-	# set Java and Resources folder
-	JavaFolder="${AppleJavaFolder}"
-	ResourcesFolder="${AppleResourcesFolder}"
-
-	APP_PACKAGE="${AppPackageFolder}"
-	JAVAROOT="${AppleJavaFolder}"
-	USER_HOME="$HOME"
-
-
-	# read the Java WorkingDirectory
-	JVMWorkDir=$(plist_get_java ':WorkingDirectory' | xargs)
-	# set Working Directory based upon PList value
-	if [[ ! -z ${JVMWorkDir} ]]; then
-		WorkingDirectory="${JVMWorkDir}"
-	else
-		# AppPackageRoot is the standard WorkingDirectory when the script is started
-		WorkingDirectory="${AppPackageRoot}"
-	fi
-	# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
-	WorkingDirectory=$(eval echo "${WorkingDirectory}")
-
-
-	# read the MainClass name
-	JVMMainClass="$(plist_get_java ':MainClass')"
-
-	# read the SplashFile name
-	JVMSplashFile=$(plist_get_java ':SplashFile')
-
-	# read the JVM Properties as an array and retain spaces
-	IFS=$'\t\n'
-	JVMOptions=($(xargs -n1 <<<$(plist_get_java ':Properties' | grep " =" | sed 's/^ */-D/g' | sed -E 's/ = (.*)$/="\1"/g')))
-	unset IFS
-	# post processing of the array follows further below...
-
-	# read the ClassPath in either Array or String style
-	JVMClassPath_RAW=$(plist_get_java ':ClassPath' | xargs)
-	if [[ $JVMClassPath_RAW == *Array* ]] ; then
-		JVMClassPath=.$(plist_get_java ':ClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
-	else
-		JVMClassPath=${JVMClassPath_RAW}
-	fi
-	# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
-	JVMClassPath=$(eval echo "${JVMClassPath}")
-
-	# read the JVM Options in either Array or String style
-	JVMDefaultOptions_RAW=$(plist_get_java ':VMOptions' | xargs)
-	if [[ $JVMDefaultOptions_RAW == *Array* ]] ; then
-		JVMDefaultOptions=$(plist_get_java ':VMOptions' | grep "    " | sed 's/^ */ /g' | tr -d '\n' | xargs)
-	else
-		JVMDefaultOptions=${JVMDefaultOptions_RAW}
-	fi
-
-	# read StartOnMainThread and add as -XstartOnFirstThread
-	JVMStartOnMainThread=$(plist_get_java ':StartOnMainThread')
-	if [ "${JVMStartOnMainThread}" == "true" ]; then
-		JVMDefaultOptions+=" -XstartOnFirstThread"
-	fi
-
-	# read the JVM Arguments as an array and retain spaces
-	IFS=$'\t\n'
-	MainArgs=($(xargs -n1 <<<$(plist_get_java ':Arguments')))
-	unset IFS
-	# post processing of the array follows further below...
-
-	# read the Java version we want to find
-	JVMVersion=$(plist_get_java ':JVMVersion' | xargs)
-	# post processing of the version string follows below...
-
-
-# read 'Info.plist' file in Oracle style
-else
-	stub_logger "[PlistStyle] Oracle"
-
-	# set Working Directory and Java and Resources folder
-	JavaFolder="${OracleJavaFolder}"
-	ResourcesFolder="${OracleResourcesFolder}"
-	WorkingDirectory="${OracleJavaFolder}"
-
-	APP_ROOT="${AppPackageFolder}"
-
-	# read the MainClass name
-	JVMMainClass="$(plist_get ':JVMMainClassName')"
-
-	# read the SplashFile name
-	JVMSplashFile=$(plist_get ':JVMSplashFile')
-
-	# read the JVM Options as an array and retain spaces
-	IFS=$'\t\n'
-	JVMOptions=($(plist_get ':JVMOptions' | grep "    " | sed 's/^ *//g'))
-	unset IFS
-	# post processing of the array follows further below...
-
-	# read the ClassPath in either Array or String style
-	JVMClassPath_RAW=$(plist_get ':JVMClassPath')
-	if [[ $JVMClassPath_RAW == *Array* ]] ; then
-		JVMClassPath=.$(plist_get ':JVMClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
-		# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
-		JVMClassPath=$(eval echo "${JVMClassPath}")
-
-	elif [[ ! -z ${JVMClassPath_RAW} ]] ; then
-		JVMClassPath=${JVMClassPath_RAW}
-		# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
-		JVMClassPath=$(eval echo "${JVMClassPath}")
-
-	else
-		#default: fallback to OracleJavaFolder
-		JVMClassPath="${JavaFolder}/*"
-		# Do NOT expand the default 'AppName.app/Contents/Java/*' classpath (#42)
-	fi
-
-	# read the JVM Default Options
-	JVMDefaultOptions=$(plist_get ':JVMDefaultOptions' | grep -o " \-.*" | tr -d '\n' | xargs)
-
-	# read the Main Arguments from JVMArguments key as an array and retain spaces (see #46 for naming details)
-	IFS=$'\t\n'
-	MainArgs=($(xargs -n1 <<<$(plist_get ':JVMArguments' | tr -d '\n' | sed -E 's/Array \{ *(.*) *\}/\1/g' | sed 's/  */ /g')))
-	unset IFS
-	# post processing of the array follows further below...
-
-	# read the Java version we want to find
-	JVMVersion=$(plist_get ':JVMVersion' | xargs)
-	# post processing of the version string follows below...
-fi
-
-
-
-# JVMVersion: post processing and optional splitting
-if [[ ${JVMVersion} == *";"* ]]; then
-	minMaxArray=(${JVMVersion//;/ })
-	JVMVersion=${minMaxArray[0]//+}
-	JVMMaxVersion=${minMaxArray[1]//+}
-fi
-stub_logger "[JavaRequirement] JVM minimum version: ${JVMVersion}"
-stub_logger "[JavaRequirement] JVM maximum version: ${JVMMaxVersion}"
-
-# MainArgs: replace occurences of $APP_ROOT with its content
-MainArgsArr=()
-for i in "${MainArgs[@]}"
-do
-	MainArgsArr+=("$(eval echo "$i")")
-done
-
-# JVMOptions: replace occurences of $APP_ROOT with its content
-JVMOptionsArr=()
-for i in "${JVMOptions[@]}"
-do
-	JVMOptionsArr+=("$(eval echo "$i")")
-done
-
-
-# internationalized messages
-############################################
-
-LANG=$(defaults read -g AppleLocale)
-stub_logger "[Language] $LANG"
-
-# French localization
-if [[ $LANG == fr* ]] ; then
-	MSG_ERROR_LAUNCHING="ERREUR au lancement de '${CFBundleName}'."
-	MSG_MISSING_MAINCLASS="'MainClass' n'est pas spécifié.\nL'application Java ne peut pas être lancée."
-	MSG_JVMVERSION_REQ_INVALID="La syntaxe de la version Java demandée est invalide: %s\nVeuillez contacter le développeur de l'application."
-	MSG_NO_SUITABLE_JAVA="La version de Java installée sur votre système ne convient pas.\nCe programme nécessite Java %s"
-	MSG_JAVA_VERSION_OR_LATER="ou ultérieur"
-	MSG_JAVA_VERSION_LATEST="(dernière mise à jour)"
-	MSG_JAVA_VERSION_MAX="à %s"
-	MSG_NO_SUITABLE_JAVA_CHECK="Merci de bien vouloir installer la version de Java requise."
-	MSG_INSTALL_JAVA="Java doit être installé sur votre système.\nRendez-vous sur java.com et suivez les instructions d'installation..."
-	MSG_LATER="Plus tard"
-	MSG_VISIT_JAVA_DOT_COM="Visiter java.com"
-
-# German localization
-elif [[ $LANG == de* ]] ; then
-	MSG_ERROR_LAUNCHING="FEHLER beim Starten von '${CFBundleName}'."
-	MSG_MISSING_MAINCLASS="Die 'MainClass' ist nicht spezifiziert!\nDie Java-Anwendung kann nicht gestartet werden!"
-	MSG_JVMVERSION_REQ_INVALID="Die Syntax der angeforderten Java-Version ist ungültig: %s\nBitte kontaktieren Sie den Entwickler der App."
-	MSG_NO_SUITABLE_JAVA="Es wurde keine passende Java-Version auf Ihrem System gefunden!\nDieses Programm benötigt Java %s"
-	MSG_JAVA_VERSION_OR_LATER="oder neuer"
-	MSG_JAVA_VERSION_LATEST="(neuste Unterversion)"
-	MSG_JAVA_VERSION_MAX="bis %s"
-	MSG_NO_SUITABLE_JAVA_CHECK="Stellen Sie sicher, dass die angeforderte Java-Version installiert ist."
-	MSG_INSTALL_JAVA="Auf Ihrem System muss die 'Java'-Software installiert sein.\nBesuchen Sie java.com für weitere Installationshinweise."
-	MSG_LATER="Später"
-	MSG_VISIT_JAVA_DOT_COM="java.com öffnen"
-
-# Simplifyed Chinese localization
-elif [[ $LANG == zh* ]] ; then
-	MSG_ERROR_LAUNCHING="无法启动 '${CFBundleName}'."
-	MSG_MISSING_MAINCLASS="没有指定 'MainClass'！\nJava程序无法启动!"
-	MSG_JVMVERSION_REQ_INVALID="Java版本参数语法错误: %s\n请联系该应用的开发者。"
-	MSG_NO_SUITABLE_JAVA="没有在系统中找到合适的Java版本！\n必须安装Java %s才能够使用该程序！"
-	MSG_JAVA_VERSION_OR_LATER="及以上版本"
-	MSG_JAVA_VERSION_LATEST="（最新版本）"
-	MSG_JAVA_VERSION_MAX="最高为 %s"
-	MSG_NO_SUITABLE_JAVA_CHECK="请确保系统中安装了所需的Java版本"
-	MSG_INSTALL_JAVA="你需要在Mac中安装Java运行环境！\n访问 java.com 了解如何安装。"
-	MSG_LATER="稍后"
-	MSG_VISIT_JAVA_DOT_COM="访问 java.com"
-
-# English default localization
-else
-	MSG_ERROR_LAUNCHING="ERROR launching '${CFBundleName}'."
-	MSG_MISSING_MAINCLASS="'MainClass' isn't specified!\nJava application cannot be started!"
-	MSG_JVMVERSION_REQ_INVALID="The syntax of the required Java version is invalid: %s\nPlease contact the App developer."
-	MSG_NO_SUITABLE_JAVA="No suitable Java version found on your system!\nThis program requires Java %s"
-	MSG_JAVA_VERSION_OR_LATER="or later"
-	MSG_JAVA_VERSION_LATEST="(latest update)"
-	MSG_JAVA_VERSION_MAX="up to %s"
-	MSG_NO_SUITABLE_JAVA_CHECK="Make sure you install the required Java version."
-	MSG_INSTALL_JAVA="You need to have JAVA installed on your Mac!\nVisit java.com for installation instructions..."
-	MSG_LATER="Later"
-	MSG_VISIT_JAVA_DOT_COM="Visit java.com"
-fi
-
-
-
-# function 'get_java_version_from_cmd()'
-#
-# returns Java version string from 'java -version' command
-# works for both old (1.8) and new (9) version schema
-#
-# @param1  path to a java JVM executable
-# @return  the Java version number as displayed in 'java -version' command
-################################################################################
-function get_java_version_from_cmd() {
-	# second sed command strips " and -ea from the version string
-	echo $("$1" -version 2>&1 | awk '/version/{print $3}' | sed -E 's/"//g;s/-ea//g')
-}
-
-
-# function 'extract_java_major_version()'
-#
-# extract Java major version from a version string
-#
-# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
-# @return  the major version (e.g. '7', '8' or '9', etc.)
-################################################################################
-function extract_java_major_version() {
-	echo $(echo "$1" | sed -E 's/^1\.//;s/^([0-9]+)(-ea|(\.[0-9_.]{1,7})?)(-b[0-9]+-[0-9]+)?[+*]?$/\1/')
-}
-
-
-# function 'get_comparable_java_version()'
-#
-# return comparable version for a Java version number or requirement string
-#
-# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
-# @return  an 8 digit numeral ('1.8.0_45'->'08000045'; '9.1.13'->'09001013')
-################################################################################
-function get_comparable_java_version() {
-	# cleaning: 1) remove leading '1.'; 2) remove build string (e.g. '-b14-468'); 3) remove 'a-Z' and '-*+' (e.g. '-ea'); 4) replace '_' with '.'
-	local cleaned=$(echo "$1" | sed -E 's/^1\.//g;s/-b[0-9]+-[0-9]+$//g;s/[a-zA-Z+*\-]//g;s/_/./g')
-	# splitting at '.' into an array
-	local arr=( ${cleaned//./ } )
-	# echo a string with left padded version numbers
-	echo "$(printf '%02s' ${arr[0]})$(printf '%03s' ${arr[1]})$(printf '%03s' ${arr[2]})"
-}
-
-
-# function 'is_valid_requirement_pattern()'
-#
-# check whether the Java requirement is a valid requirement pattern
-#
-# supported requirements are for example:
-# - 1.6       requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
-# - 1.6*      requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
-# - 1.6+      requires Java 6 or higher         [1.6, 1.6.0_45, 1.8, 9, etc.]
-# - 1.6.0     requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
-# - 1.6.0_45  requires Java 6u45                [1.6.0_45]
-# - 1.6.0_45+ requires Java 6u45 or higher      [1.6.0_45, 1.6.0_88, 1.8, etc.]
-# - 9         requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
-# - 9*        requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
-# - 9+        requires Java 9 or higher         [9.0, 9.1, 10, etc.]
-# - 9.1       requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
-# - 9.1*      requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
-# - 9.1+      requires Java 9.1 or higher       [9.1, 9.2, 10, etc.]
-# - 9.1.3     requires Java 9.1.3               [9.1.3]
-# - 9.1.3*    requires Java 9.1.3 (any update)  [9.1.3]
-# - 9.1.3+    requires Java 9.1.3 or higher     [9.1.3, 9.1.4, 9.2.*, 10, etc.]
-# - 10-ea     requires Java 10 (early access release)
-#
-# unsupported requirement patterns are for example:
-# - 1.2, 1.3, 1.9       Java 2, 3 are not supported
-# - 1.9                 Java 9 introduced a new versioning scheme
-# - 6u45                known versioning syntax, but unsupported
-# - 9-ea*, 9-ea+        early access releases paired with */+
-# - 9., 9.*, 9.+        version ending with a .
-# - 9.1., 9.1.*, 9.1.+  version ending with a .
-# - 9.3.5.6             4 part version number is unsupported
-#
-# @param1  a Java requirement string ('1.8+')
-# @return  boolean exit code: 0 (is valid), 1 (is not valid)
-################################################################################
-function is_valid_requirement_pattern() {
-	local java_req=$1
-	java8pattern='1\.[4-8](\.0)?(\.0_[0-9]+)?[*+]?'
-	java9pattern='(9|1[0-9])(-ea|[*+]|(\.[0-9]+){1,2}[*+]?)?'
-	# test matches either old Java versioning scheme (up to 1.8) or new scheme (starting with 9)
-	if [[ ${java_req} =~ ^(${java8pattern}|${java9pattern})$ ]]; then
-		return 0
-	else
-		return 1
-	fi
-}
-
-
-
-# determine which JVM to use
-############################################
-
-JAVACMD="${AppPackageFolder}/../jre1.8.0_262/bin/java"
-
-
-# log the Java Command and the extracted version number
-stub_logger "[JavaCommand] '$JAVACMD'"
-stub_logger "[JavaVersion] $(get_java_version_from_cmd "${JAVACMD}")${JAVACMD_version:+ / $JAVACMD_version}"
-
-
-
-if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then
-
-	# different error messages when a specific JVM was required
-	if [ ! -z "${JVMVersion}" ] ; then
-		# display human readable java version (#28)
-		java_version_hr=$(echo ${JVMVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+/ ${MSG_JAVA_VERSION_OR_LATER}/;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
-		MSG_NO_SUITABLE_JAVA_EXPANDED=$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}").
-
-		if [ ! -z "${JVMMaxVersion}" ] ; then
-			java_version_hr=$(extract_java_major_version ${JVMVersion})
-			java_version_max_hr=$(echo ${JVMMaxVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+//;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
-			MSG_NO_SUITABLE_JAVA_EXPANDED="$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}") $(printf "${MSG_JAVA_VERSION_MAX}" "${java_version_max_hr}")"
-		fi
-
-		# log exit cause
-		stub_logger "[EXIT 3] ${MSG_NO_SUITABLE_JAVA_EXPANDED}"
-
-		# display error message with AppleScript
-		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_NO_SUITABLE_JAVA_EXPANDED}\n${MSG_NO_SUITABLE_JAVA_CHECK}\" with title \"${CFBundleName}\"  buttons {\" OK \", \"${MSG_VISIT_JAVA_DOT_COM}\"} default button \"${MSG_VISIT_JAVA_DOT_COM}\" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" \
-				-e "set response to button returned of the result" \
-				-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"http://java.com\""
-		# exit with error
-		exit 3
-
-	else
-		# log exit cause
-		stub_logger "[EXIT 1] ${MSG_ERROR_LAUNCHING}"
-		# display error message with AppleScript
-		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_INSTALL_JAVA}\" with title \"${CFBundleName}\" buttons {\"${MSG_LATER}\", \"${MSG_VISIT_JAVA_DOT_COM}\"} default button \"${MSG_VISIT_JAVA_DOT_COM}\" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" \
-					-e "set response to button returned of the result" \
-					-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"http://java.com\""
-		# exit with error
-		exit 1
-	fi
-fi
-
-
-
-# MainClass check
-############################################
-
-if [ -z "${JVMMainClass}" ]; then
-	# log exit cause
-	stub_logger "[EXIT 2] ${MSG_MISSING_MAINCLASS}"
-	# display error message with AppleScript
-	osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_MISSING_MAINCLASS}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
-	# exit with error
-	exit 2
-fi
-
-
-
-# execute $JAVACMD and do some preparation
-############################################
-
-# enable drag&drop to the dock icon
-export CFProcessPath="$0"
-
-# remove Apples ProcessSerialNumber from passthru arguments (#39)
-if [[ "$*" == -psn* ]] ; then
-	ArgsPassthru=()
-else
-	ArgsPassthru=("$@")
-fi
-
-# change to Working Directory based upon Apple/Oracle Plist info
-cd "${WorkingDirectory}" || exit 13
-stub_logger "[WorkingDirectory] ${WorkingDirectory}"
-
-# execute Java and set
-# - classpath
-# - splash image
-# - dock icon
-# - app name
-# - JVM options / properties (-D)
-# - JVM default options (-X)
-# - main class
-# - main class arguments
-# - passthrough arguments from Terminal or Drag'n'Drop to Finder icon
-stub_logger "[Exec] \"$JAVACMD\" -cp \"${JVMClassPath}\" -splash:\"${ResourcesFolder}/${JVMSplashFile}\" -Xdock:icon=\"${ResourcesFolder}/${CFBundleIconFile}\" -Xdock:name=\"${CFBundleName}\" ${JVMOptionsArr:+$(printf "'%s' " "${JVMOptionsArr[@]}") }${JVMDefaultOptions:+$JVMDefaultOptions }${JVMMainClass}${MainArgsArr:+ $(printf "'%s' " "${MainArgsArr[@]}")}${ArgsPassthru:+ $(printf "'%s' " "${ArgsPassthru[@]}")}"
-exec "${JAVACMD}" \
-		-cp "${JVMClassPath}" \
-		-splash:"${ResourcesFolder}/${JVMSplashFile}" \
-		-Xdock:icon="${ResourcesFolder}/${CFBundleIconFile}" \
-		-Xdock:name="${CFBundleName}" \
-		${JVMOptions:+"${JVMOptions[@]}" }\
-		${JVMDefaultOptions:+$JVMDefaultOptions }\
-		"${JVMMainClass}"\
-		${MainArgsArr:+ "${MainArgsArr[@]}"}\
-		${ArgsPassthru:+ "${ArgsPassthru[@]}"}
diff -Nru beast2-mcmc-2.6.6+dfsg/release/Mac/universalJavaApplicationStub beast2-mcmc-2.6.7+dfsg/release/Mac/universalJavaApplicationStub
--- beast2-mcmc-2.6.6+dfsg/release/Mac/universalJavaApplicationStub	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/release/Mac/universalJavaApplicationStub	1970-01-01 00:00:00.000000000 +0000
@@ -1,774 +0,0 @@
-#!/bin/bash
-##################################################################################
-#                                                                                #
-# universalJavaApplicationStub                                                   #
-#                                                                                #
-# A BASH based JavaApplicationStub for Java Apps on Mac OS X                     #
-# that works with both Apple's and Oracle's plist format.                        #
-#                                                                                #
-# Inspired by Ian Roberts stackoverflow answer                                   #
-# at http://stackoverflow.com/a/17546508/1128689                                 #
-#                                                                                #
-# @author    Tobias Fischer                                                      #
-# @url       https://github.com/tofi86/universalJavaApplicationStub              #
-# @date      2018-07-29                                                          #
-# @version   3.0.3                                                               #
-#                                                                                #
-##################################################################################
-#                                                                                #
-# The MIT License (MIT)                                                          #
-#                                                                                #
-# Copyright (c) 2014-2018 Tobias Fischer                                         #
-#                                                                                #
-# Permission is hereby granted, free of charge, to any person obtaining a copy   #
-# of this software and associated documentation files (the "Software"), to deal  #
-# in the Software without restriction, including without limitation the rights   #
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell      #
-# copies of the Software, and to permit persons to whom the Software is          #
-# furnished to do so, subject to the following conditions:                       #
-#                                                                                #
-# The above copyright notice and this permission notice shall be included in all #
-# copies or substantial portions of the Software.                                #
-#                                                                                #
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR     #
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,       #
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE    #
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER         #
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  #
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE  #
-# SOFTWARE.                                                                      #
-#                                                                                #
-##################################################################################
-
-
-
-# function 'stub_logger()'
-#
-# A logger which logs to the macOS Console.app using the 'syslog' command
-#
-# @param1  the log message
-# @return  void
-################################################################################
-function stub_logger() {
-	syslog -s -k \
-		Facility com.apple.console \
-		Level Notice \
-		Sender "$(basename "$0")" \
-		Message "[$$][${CFBundleName:-$(basename "$0")}] $1"
-}
-
-
-
-# set the directory abspath of the current
-# shell script with symlinks being resolved
-############################################
-
-PRG=$0
-while [ -h "$PRG" ]; do
-	ls=$(ls -ld "$PRG")
-	link=$(expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null)
-	if expr "$link" : '^/' 2> /dev/null >/dev/null; then
-		PRG="$link"
-	else
-		PRG="$(dirname "$PRG")/$link"
-	fi
-done
-PROGDIR=$(dirname "$PRG")
-stub_logger "[StubDir] $PROGDIR"
-
-
-
-# set files and folders
-############################################
-
-# the absolute path of the app package
-cd "$PROGDIR"/../../ || exit 11
-AppPackageFolder=$(pwd)
-
-# the base path of the app package
-cd .. || exit 12
-AppPackageRoot=$(pwd)
-
-# set Apple's Java folder
-AppleJavaFolder="${AppPackageFolder}"/Contents/Resources/Java
-
-# set Apple's Resources folder
-AppleResourcesFolder="${AppPackageFolder}"/Contents/Resources
-
-# set Oracle's Java folder
-OracleJavaFolder="${AppPackageFolder}"/Contents/Java
-
-# set Oracle's Resources folder
-OracleResourcesFolder="${AppPackageFolder}"/Contents/Resources
-
-# set path to Info.plist in bundle
-InfoPlistFile="${AppPackageFolder}"/Contents/Info.plist
-
-# set the default JVM Version to a null string
-JVMVersion=""
-JVMMaxVersion=""
-
-
-
-# function 'plist_get()'
-#
-# read a specific Plist key with 'PlistBuddy' utility
-#
-# @param1  the Plist key with leading colon ':'
-# @return  the value as String or Array
-################################################################################
-plist_get(){
-	/usr/libexec/PlistBuddy -c "print $1" "${InfoPlistFile}" 2> /dev/null
-}
-
-# function 'plist_get_java()'
-#
-# read a specific Plist key with 'PlistBuddy' utility
-# in the 'Java' or 'JavaX' dictionary (<dict>)
-#
-# @param1  the Plist :Java(X):Key with leading colon ':'
-# @return  the value as String or Array
-################################################################################
-plist_get_java(){
-	plist_get ${JavaKey:-":Java"}$1
-}
-
-
-
-# read Info.plist and extract JVM options
-############################################
-
-# read the program name from CFBundleName
-CFBundleName=$(plist_get ':CFBundleName')
-
-# read the icon file name
-CFBundleIconFile=$(plist_get ':CFBundleIconFile')
-
-
-# check Info.plist for Apple style Java keys -> if key :Java is present, parse in apple mode
-/usr/libexec/PlistBuddy -c "print :Java" "${InfoPlistFile}" > /dev/null 2>&1
-exitcode=$?
-JavaKey=":Java"
-
-# if no :Java key is present, check Info.plist for universalJavaApplication style JavaX keys -> if key :JavaX is present, parse in apple mode
-if [ $exitcode -ne 0 ]; then
-	/usr/libexec/PlistBuddy -c "print :JavaX" "${InfoPlistFile}" > /dev/null 2>&1
-	exitcode=$?
-	JavaKey=":JavaX"
-fi
-
-
-# read 'Info.plist' file in Apple style if exit code returns 0 (true, ':Java' key is present)
-if [ $exitcode -eq 0 ]; then
-	stub_logger "[PlistStyle] Apple"
-
-	# set Java and Resources folder
-	JavaFolder="${AppleJavaFolder}"
-	ResourcesFolder="${AppleResourcesFolder}"
-
-	APP_PACKAGE="${AppPackageFolder}"
-	JAVAROOT="${AppleJavaFolder}"
-	USER_HOME="$HOME"
-
-
-	# read the Java WorkingDirectory
-	JVMWorkDir=$(plist_get_java ':WorkingDirectory' | xargs)
-	# set Working Directory based upon PList value
-	if [[ ! -z ${JVMWorkDir} ]]; then
-		WorkingDirectory="${JVMWorkDir}"
-	else
-		# AppPackageRoot is the standard WorkingDirectory when the script is started
-		WorkingDirectory="${AppPackageRoot}"
-	fi
-	# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
-	WorkingDirectory=$(eval echo "${WorkingDirectory}")
-
-
-	# read the MainClass name
-	JVMMainClass="$(plist_get_java ':MainClass')"
-
-	# read the SplashFile name
-	JVMSplashFile=$(plist_get_java ':SplashFile')
-
-	# read the JVM Properties as an array and retain spaces
-	IFS=$'\t\n'
-	JVMOptions=($(xargs -n1 <<<$(plist_get_java ':Properties' | grep " =" | sed 's/^ */-D/g' | sed -E 's/ = (.*)$/="\1"/g')))
-	unset IFS
-	# post processing of the array follows further below...
-
-	# read the ClassPath in either Array or String style
-	JVMClassPath_RAW=$(plist_get_java ':ClassPath' | xargs)
-	if [[ $JVMClassPath_RAW == *Array* ]] ; then
-		JVMClassPath=.$(plist_get_java ':ClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
-	else
-		JVMClassPath=${JVMClassPath_RAW}
-	fi
-	# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
-	JVMClassPath=$(eval echo "${JVMClassPath}")
-
-	# read the JVM Options in either Array or String style
-	JVMDefaultOptions_RAW=$(plist_get_java ':VMOptions' | xargs)
-	if [[ $JVMDefaultOptions_RAW == *Array* ]] ; then
-		JVMDefaultOptions=$(plist_get_java ':VMOptions' | grep "    " | sed 's/^ */ /g' | tr -d '\n' | xargs)
-	else
-		JVMDefaultOptions=${JVMDefaultOptions_RAW}
-	fi
-
-	# read StartOnMainThread and add as -XstartOnFirstThread
-	JVMStartOnMainThread=$(plist_get_java ':StartOnMainThread')
-	if [ "${JVMStartOnMainThread}" == "true" ]; then
-		JVMDefaultOptions+=" -XstartOnFirstThread"
-	fi
-
-	# read the JVM Arguments as an array and retain spaces
-	IFS=$'\t\n'
-	MainArgs=($(xargs -n1 <<<$(plist_get_java ':Arguments')))
-	unset IFS
-	# post processing of the array follows further below...
-
-	# read the Java version we want to find
-	JVMVersion=$(plist_get_java ':JVMVersion' | xargs)
-	# post processing of the version string follows below...
-
-
-# read 'Info.plist' file in Oracle style
-else
-	stub_logger "[PlistStyle] Oracle"
-
-	# set Working Directory and Java and Resources folder
-	JavaFolder="${OracleJavaFolder}"
-	ResourcesFolder="${OracleResourcesFolder}"
-	WorkingDirectory="${OracleJavaFolder}"
-
-	APP_ROOT="${AppPackageFolder}"
-
-	# read the MainClass name
-	JVMMainClass="$(plist_get ':JVMMainClassName')"
-
-	# read the SplashFile name
-	JVMSplashFile=$(plist_get ':JVMSplashFile')
-
-	# read the JVM Options as an array and retain spaces
-	IFS=$'\t\n'
-	JVMOptions=($(plist_get ':JVMOptions' | grep "    " | sed 's/^ *//g'))
-	unset IFS
-	# post processing of the array follows further below...
-
-	# read the ClassPath in either Array or String style
-	JVMClassPath_RAW=$(plist_get ':JVMClassPath')
-	if [[ $JVMClassPath_RAW == *Array* ]] ; then
-		JVMClassPath=.$(plist_get ':JVMClassPath' | grep "    " | sed 's/^ */:/g' | tr -d '\n' | xargs)
-		# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
-		JVMClassPath=$(eval echo "${JVMClassPath}")
-
-	elif [[ ! -z ${JVMClassPath_RAW} ]] ; then
-		JVMClassPath=${JVMClassPath_RAW}
-		# expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME
-		JVMClassPath=$(eval echo "${JVMClassPath}")
-
-	else
-		#default: fallback to OracleJavaFolder
-		JVMClassPath="${JavaFolder}/*"
-		# Do NOT expand the default 'AppName.app/Contents/Java/*' classpath (#42)
-	fi
-
-	# read the JVM Default Options
-	JVMDefaultOptions=$(plist_get ':JVMDefaultOptions' | grep -o " \-.*" | tr -d '\n' | xargs)
-
-	# read the Main Arguments from JVMArguments key as an array and retain spaces (see #46 for naming details)
-	IFS=$'\t\n'
-	MainArgs=($(xargs -n1 <<<$(plist_get ':JVMArguments' | tr -d '\n' | sed -E 's/Array \{ *(.*) *\}/\1/g' | sed 's/  */ /g')))
-	unset IFS
-	# post processing of the array follows further below...
-
-	# read the Java version we want to find
-	JVMVersion=$(plist_get ':JVMVersion' | xargs)
-	# post processing of the version string follows below...
-fi
-
-
-
-# JVMVersion: post processing and optional splitting
-if [[ ${JVMVersion} == *";"* ]]; then
-	minMaxArray=(${JVMVersion//;/ })
-	JVMVersion=${minMaxArray[0]//+}
-	JVMMaxVersion=${minMaxArray[1]//+}
-fi
-stub_logger "[JavaRequirement] JVM minimum version: ${JVMVersion}"
-stub_logger "[JavaRequirement] JVM maximum version: ${JVMMaxVersion}"
-
-# MainArgs: replace occurences of $APP_ROOT with its content
-MainArgsArr=()
-for i in "${MainArgs[@]}"
-do
-	MainArgsArr+=("$(eval echo "$i")")
-done
-
-# JVMOptions: replace occurences of $APP_ROOT with its content
-JVMOptionsArr=()
-for i in "${JVMOptions[@]}"
-do
-	JVMOptionsArr+=("$(eval echo "$i")")
-done
-
-
-# internationalized messages
-############################################
-
-LANG=$(defaults read -g AppleLocale)
-stub_logger "[Language] $LANG"
-
-# French localization
-if [[ $LANG == fr* ]] ; then
-	MSG_ERROR_LAUNCHING="ERREUR au lancement de '${CFBundleName}'."
-	MSG_MISSING_MAINCLASS="'MainClass' n'est pas spécifié.\nL'application Java ne peut pas être lancée."
-	MSG_JVMVERSION_REQ_INVALID="La syntaxe de la version Java demandée est invalide: %s\nVeuillez contacter le développeur de l'application."
-	MSG_NO_SUITABLE_JAVA="La version de Java installée sur votre système ne convient pas.\nCe programme nécessite Java %s"
-	MSG_JAVA_VERSION_OR_LATER="ou ultérieur"
-	MSG_JAVA_VERSION_LATEST="(dernière mise à jour)"
-	MSG_JAVA_VERSION_MAX="à %s"
-	MSG_NO_SUITABLE_JAVA_CHECK="Merci de bien vouloir installer la version de Java requise."
-	MSG_INSTALL_JAVA="Java doit être installé sur votre système.\nRendez-vous sur java.com et suivez les instructions d'installation..."
-	MSG_LATER="Plus tard"
-	MSG_VISIT_JAVA_DOT_COM="Visiter java.com"
-
-# German localization
-elif [[ $LANG == de* ]] ; then
-	MSG_ERROR_LAUNCHING="FEHLER beim Starten von '${CFBundleName}'."
-	MSG_MISSING_MAINCLASS="Die 'MainClass' ist nicht spezifiziert!\nDie Java-Anwendung kann nicht gestartet werden!"
-	MSG_JVMVERSION_REQ_INVALID="Die Syntax der angeforderten Java-Version ist ungültig: %s\nBitte kontaktieren Sie den Entwickler der App."
-	MSG_NO_SUITABLE_JAVA="Es wurde keine passende Java-Version auf Ihrem System gefunden!\nDieses Programm benötigt Java %s"
-	MSG_JAVA_VERSION_OR_LATER="oder neuer"
-	MSG_JAVA_VERSION_LATEST="(neuste Unterversion)"
-	MSG_JAVA_VERSION_MAX="bis %s"
-	MSG_NO_SUITABLE_JAVA_CHECK="Stellen Sie sicher, dass die angeforderte Java-Version installiert ist."
-	MSG_INSTALL_JAVA="Auf Ihrem System muss die 'Java'-Software installiert sein.\nBesuchen Sie java.com für weitere Installationshinweise."
-	MSG_LATER="Später"
-	MSG_VISIT_JAVA_DOT_COM="java.com öffnen"
-
-# Simplifyed Chinese localization
-elif [[ $LANG == zh* ]] ; then
-	MSG_ERROR_LAUNCHING="无法启动 '${CFBundleName}'."
-	MSG_MISSING_MAINCLASS="没有指定 'MainClass'！\nJava程序无法启动!"
-	MSG_JVMVERSION_REQ_INVALID="Java版本参数语法错误: %s\n请联系该应用的开发者。"
-	MSG_NO_SUITABLE_JAVA="没有在系统中找到合适的Java版本！\n必须安装Java %s才能够使用该程序！"
-	MSG_JAVA_VERSION_OR_LATER="及以上版本"
-	MSG_JAVA_VERSION_LATEST="（最新版本）"
-	MSG_JAVA_VERSION_MAX="最高为 %s"
-	MSG_NO_SUITABLE_JAVA_CHECK="请确保系统中安装了所需的Java版本"
-	MSG_INSTALL_JAVA="你需要在Mac中安装Java运行环境！\n访问 java.com 了解如何安装。"
-	MSG_LATER="稍后"
-	MSG_VISIT_JAVA_DOT_COM="访问 java.com"
-
-# English default localization
-else
-	MSG_ERROR_LAUNCHING="ERROR launching '${CFBundleName}'."
-	MSG_MISSING_MAINCLASS="'MainClass' isn't specified!\nJava application cannot be started!"
-	MSG_JVMVERSION_REQ_INVALID="The syntax of the required Java version is invalid: %s\nPlease contact the App developer."
-	MSG_NO_SUITABLE_JAVA="No suitable Java version found on your system!\nThis program requires Java %s"
-	MSG_JAVA_VERSION_OR_LATER="or later"
-	MSG_JAVA_VERSION_LATEST="(latest update)"
-	MSG_JAVA_VERSION_MAX="up to %s"
-	MSG_NO_SUITABLE_JAVA_CHECK="Make sure you install the required Java version."
-	MSG_INSTALL_JAVA="You need to have JAVA installed on your Mac!\nVisit java.com for installation instructions..."
-	MSG_LATER="Later"
-	MSG_VISIT_JAVA_DOT_COM="Visit java.com"
-fi
-
-
-
-# function 'get_java_version_from_cmd()'
-#
-# returns Java version string from 'java -version' command
-# works for both old (1.8) and new (9) version schema
-#
-# @param1  path to a java JVM executable
-# @return  the Java version number as displayed in 'java -version' command
-################################################################################
-function get_java_version_from_cmd() {
-	# second sed command strips " and -ea from the version string
-	echo $("$1" -version 2>&1 | awk '/version/{print $3}' | sed -E 's/"//g;s/-ea//g')
-}
-
-
-# function 'extract_java_major_version()'
-#
-# extract Java major version from a version string
-#
-# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
-# @return  the major version (e.g. '7', '8' or '9', etc.)
-################################################################################
-function extract_java_major_version() {
-	echo $(echo "$1" | sed -E 's/^1\.//;s/^([0-9]+)(-ea|(\.[0-9_.]{1,7})?)(-b[0-9]+-[0-9]+)?[+*]?$/\1/')
-}
-
-
-# function 'get_comparable_java_version()'
-#
-# return comparable version for a Java version number or requirement string
-#
-# @param1  a Java version number ('1.8.0_45') or requirement string ('1.8+')
-# @return  an 8 digit numeral ('1.8.0_45'->'08000045'; '9.1.13'->'09001013')
-################################################################################
-function get_comparable_java_version() {
-	# cleaning: 1) remove leading '1.'; 2) remove build string (e.g. '-b14-468'); 3) remove 'a-Z' and '-*+' (e.g. '-ea'); 4) replace '_' with '.'
-	local cleaned=$(echo "$1" | sed -E 's/^1\.//g;s/-b[0-9]+-[0-9]+$//g;s/[a-zA-Z+*\-]//g;s/_/./g')
-	# splitting at '.' into an array
-	local arr=( ${cleaned//./ } )
-	# echo a string with left padded version numbers
-	echo "$(printf '%02s' ${arr[0]})$(printf '%03s' ${arr[1]})$(printf '%03s' ${arr[2]})"
-}
-
-
-# function 'is_valid_requirement_pattern()'
-#
-# check whether the Java requirement is a valid requirement pattern
-#
-# supported requirements are for example:
-# - 1.6       requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
-# - 1.6*      requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
-# - 1.6+      requires Java 6 or higher         [1.6, 1.6.0_45, 1.8, 9, etc.]
-# - 1.6.0     requires Java 6 (any update)      [1.6, 1.6.0_45, 1.6.0_88]
-# - 1.6.0_45  requires Java 6u45                [1.6.0_45]
-# - 1.6.0_45+ requires Java 6u45 or higher      [1.6.0_45, 1.6.0_88, 1.8, etc.]
-# - 9         requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
-# - 9*        requires Java 9 (any update)      [9.0.*, 9.1, 9.3, etc.]
-# - 9+        requires Java 9 or higher         [9.0, 9.1, 10, etc.]
-# - 9.1       requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
-# - 9.1*      requires Java 9.1 (any update)    [9.1.*, 9.1.2, 9.1.13, etc.]
-# - 9.1+      requires Java 9.1 or higher       [9.1, 9.2, 10, etc.]
-# - 9.1.3     requires Java 9.1.3               [9.1.3]
-# - 9.1.3*    requires Java 9.1.3 (any update)  [9.1.3]
-# - 9.1.3+    requires Java 9.1.3 or higher     [9.1.3, 9.1.4, 9.2.*, 10, etc.]
-# - 10-ea     requires Java 10 (early access release)
-#
-# unsupported requirement patterns are for example:
-# - 1.2, 1.3, 1.9       Java 2, 3 are not supported
-# - 1.9                 Java 9 introduced a new versioning scheme
-# - 6u45                known versioning syntax, but unsupported
-# - 9-ea*, 9-ea+        early access releases paired with */+
-# - 9., 9.*, 9.+        version ending with a .
-# - 9.1., 9.1.*, 9.1.+  version ending with a .
-# - 9.3.5.6             4 part version number is unsupported
-#
-# @param1  a Java requirement string ('1.8+')
-# @return  boolean exit code: 0 (is valid), 1 (is not valid)
-################################################################################
-function is_valid_requirement_pattern() {
-	local java_req=$1
-	java8pattern='1\.[4-8](\.0)?(\.0_[0-9]+)?[*+]?'
-	java9pattern='(9|1[0-9])(-ea|[*+]|(\.[0-9]+){1,2}[*+]?)?'
-	# test matches either old Java versioning scheme (up to 1.8) or new scheme (starting with 9)
-	if [[ ${java_req} =~ ^(${java8pattern}|${java9pattern})$ ]]; then
-		return 0
-	else
-		return 1
-	fi
-}
-
-
-
-# determine which JVM to use
-############################################
-
-# default Apple JRE plugin path (< 1.6)
-apple_jre_plugin="/Library/Java/Home/bin/java"
-apple_jre_version=$(get_java_version_from_cmd "${apple_jre_plugin}")
-# default Oracle JRE plugin path (>= 1.7)
-oracle_jre_plugin="/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java"
-oracle_jre_version=$(get_java_version_from_cmd "${oracle_jre_plugin}")
-
-
-# first check system variable "$JAVA_HOME" -> has precedence over any other System JVM
-stub_logger '[JavaSearch] Checking for $JAVA_HOME ...'
-if [ -n "$JAVA_HOME" ] ; then
-	stub_logger "[JavaSearch] ... found JAVA_HOME with value $JAVA_HOME"
-
-	# PR 26: Allow specifying "$JAVA_HOME" relative to "$AppPackageFolder"
-	# which allows for bundling a custom version of Java inside your app!
-	if [[ $JAVA_HOME == /* ]] ; then
-		# if "$JAVA_HOME" starts with a Slash it's an absolute path
-		JAVACMD="$JAVA_HOME/bin/java"
-	else
-		# otherwise it's a relative path to "$AppPackageFolder"
-		JAVACMD="$AppPackageFolder/$JAVA_HOME/bin/java"
-	fi
-	JAVACMD_version=$(get_comparable_java_version $(get_java_version_from_cmd "${JAVACMD}"))
-else
-	stub_logger "[JavaSearch] ... didn't found JAVA_HOME"
-fi
-
-
-# check for any other or a specific Java version
-# also if $JAVA_HOME exists but isn't executable
-if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then
-	stub_logger "[JavaSearch] Checking for JavaVirtualMachines on the system ..."
-	# reset variables
-	JAVACMD=""
-	JAVACMD_version=""
-
-	# first check whether JVMVersion string is a valid requirement string
-	if [ ! -z "${JVMVersion}" ] && ! is_valid_requirement_pattern ${JVMVersion} ; then
-		MSG_JVMVERSION_REQ_INVALID_EXPANDED=$(printf "${MSG_JVMVERSION_REQ_INVALID}" "${JVMVersion}")
-		# log exit cause
-		stub_logger "[EXIT 4] ${MSG_JVMVERSION_REQ_INVALID_EXPANDED}"
-		# display error message with AppleScript
-		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_JVMVERSION_REQ_INVALID_EXPANDED}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
-		# exit with error
-		exit 4
-	fi
-	# then check whether JVMMaxVersion string is a valid requirement string
-	if [ ! -z "${JVMMaxVersion}" ] && ! is_valid_requirement_pattern ${JVMMaxVersion} ; then
-		MSG_JVMVERSION_REQ_INVALID_EXPANDED=$(printf "${MSG_JVMVERSION_REQ_INVALID}" "${JVMMaxVersion}")
-		# log exit cause
-		stub_logger "[EXIT 5] ${MSG_JVMVERSION_REQ_INVALID_EXPANDED}"
-		# display error message with AppleScript
-		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_JVMVERSION_REQ_INVALID_EXPANDED}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
-		# exit with error
-		exit 5
-	fi
-
-
-	# find installed JavaVirtualMachines (JDK + JRE)
-	allJVMs=()
-	# read JDK's from '/usr/libexec/java_home -V' command
-	while read -r line; do
-		version=$(echo $line | awk -F $',' '{print $1;}')
-		path=$(echo $line | awk -F $'" ' '{print $2;}')
-		path+="/bin/java"
-		allJVMs+=("$version:$path")
-	done < <(/usr/libexec/java_home -V 2>&1 | grep '^[[:space:]]')
-	# unset while loop variables
-	unset version path
-
-	# add Apple JRE if available
-	if [ -x "${apple_jre_plugin}" ] ; then
-		allJVMs+=("$apple_jre_version:$apple_jre_plugin")
-	fi
-
-	# add Oracle JRE if available
-	if [ -x "${oracle_jre_plugin}" ] ; then
-		allJVMs+=("$oracle_jre_version:$oracle_jre_plugin")
-	fi
-
-	# debug output
-	for i in "${allJVMs[@]}"
-	do
-		stub_logger "[JavaSearch] ... found JVM: $i"
-	done
-
-
-	# determine JVMs matching the min/max version requirement
-	minC=$(get_comparable_java_version ${JVMVersion})
-	maxC=$(get_comparable_java_version ${JVMMaxVersion})
-	matchingJVMs=()
-
-	for i in "${allJVMs[@]}"
-	do
-		# split JVM string at ':' delimiter to retain spaces in $path substring
-		IFS=: arr=($i) ; unset IFS
-		# [0] JVM version number
-		ver=${arr[0]}
-		# comparable JVM version number
-		comp=$(get_comparable_java_version $ver)
-		# [1] JVM path
-		path="${arr[1]}"
-		# construct string item for adding to the "matchingJVMs" array
-		item="$comp:$ver:$path"
-
-		# pre-requisite: current version number needs to be greater than min version number
-		if [ "$comp" -ge "$minC" ] ; then
-
-			# perform max version checks if max version requirement is present
-			if [ ! -z ${JVMMaxVersion} ] ; then
-
-				# max version requirement ends with '*' modifier
-				if [[ ${JVMMaxVersion} == *\* ]] ; then
-
-					# use the '*' modifier from the max version string as wildcard for a 'starts with' comparison
-					# and check whether the current version number starts with the max version wildcard string
-					if [[ ${ver} == ${JVMMaxVersion} ]]; then
-						matchingJVMs+=("$item")
-
-					# or whether the current comparable version is lower than the comparable max version
-					elif [ "$comp" -le "$maxC" ] ; then
-						matchingJVMs+=("$item")
-					fi
-
-				# max version requirement ends with '+' modifier -> always add this version if it's greater than $min
-				# because a max requirement with + modifier doesn't make sense
-				elif [[ ${JVMMaxVersion} == *+ ]] ; then
-					matchingJVMs+=("$item")
-
-				# matches 6 zeros at the end of the max version string (e.g. for 1.8, 9)
-				# -> then the max version string should be treated like with a '*' modifier at the end
-				#elif [[ ${maxC} =~ ^[0-9]{2}0{6}$ ]] && [ "$comp" -le $(( ${maxC#0} + 999 )) ] ; then
-				#	matchingJVMs+=("$item")
-
-				# matches 3 zeros at the end of the max version string (e.g. for 9.1, 10.3)
-				# -> then the max version string should be treated like with a '*' modifier at the end
-				#elif [[ ${maxC} =~ ^[0-9]{5}0{3}$ ]] && [ "$comp" -le "${maxC}" ] ; then
-				#	matchingJVMs+=("$item")
-
-				# matches standard requirements without modifier
-				elif [ "$comp" -le "$maxC" ]; then
-					matchingJVMs+=("$item")
-				fi
-
-			# no max version requirement:
-
-			# min version requirement ends with '+' modifier
-			# -> always add the current version because it's greater than $min
-			elif [[ ${JVMVersion} == *+ ]] ; then
-				matchingJVMs+=("$item")
-
-			# min version requirement ends with '*' modifier
-			# -> use the '*' modifier from the min version string as wildcard for a 'starts with' comparison
-			#    and check whether the current version number starts with the min version wildcard string
-			elif [[ ${JVMVersion} == *\* ]] ; then
-				if [[ ${ver} == ${JVMVersion} ]] ; then
-					matchingJVMs+=("$item")
-				fi
-
-			# compare the min version against the current version with an additional * wildcard for a 'starts with' comparison
-			# -> e.g. add 1.8.0_44 when the requirement is 1.8
-			elif [[ ${ver} == ${JVMVersion}* ]] ; then
-					matchingJVMs+=("$item")
-			fi
-		fi
-	done
-	# unset for loop variables
-	unset arr ver comp path item
-
-	# debug output
-	for i in "${matchingJVMs[@]}"
-	do
-		stub_logger "[JavaSearch] ... ... matches all requirements: $i"
-	done
-
-
-	# sort the matching JavaVirtualMachines by version number
-	# https://stackoverflow.com/a/11789688/1128689
-	IFS=$'\n' matchingJVMs=($(sort -nr <<<"${matchingJVMs[*]}"))
-	unset IFS
-
-
-	# get the highest matching JVM
-	for ((i = 0; i < ${#matchingJVMs[@]}; i++));
-	do
-		# split JVM string at ':' delimiter to retain spaces in $path substring
-		IFS=: arr=(${matchingJVMs[$i]}) ; unset IFS
-		# [0] comparable JVM version number
-		comp=${arr[0]}
-		# [1] JVM version number
-		ver=${arr[1]}
-		# [2] JVM path
-		path="${arr[2]}"
-
-		# use current value as JAVACMD if it's executable
-		if [ -x "$path" ] ; then
-			JAVACMD="$path"
-			JAVACMD_version=$comp
-			break
-		fi
-	done
-	# unset for loop variables
-	unset arr comp ver path
-fi
-
-# log the Java Command and the extracted version number
-stub_logger "[JavaCommand] '$JAVACMD'"
-stub_logger "[JavaVersion] $(get_java_version_from_cmd "${JAVACMD}")${JAVACMD_version:+ / $JAVACMD_version}"
-
-
-
-if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then
-
-	# different error messages when a specific JVM was required
-	if [ ! -z "${JVMVersion}" ] ; then
-		# display human readable java version (#28)
-		java_version_hr=$(echo ${JVMVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+/ ${MSG_JAVA_VERSION_OR_LATER}/;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
-		MSG_NO_SUITABLE_JAVA_EXPANDED=$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}").
-
-		if [ ! -z "${JVMMaxVersion}" ] ; then
-			java_version_hr=$(extract_java_major_version ${JVMVersion})
-			java_version_max_hr=$(echo ${JVMMaxVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+//;s/*/ ${MSG_JAVA_VERSION_LATEST}/")
-			MSG_NO_SUITABLE_JAVA_EXPANDED="$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}") $(printf "${MSG_JAVA_VERSION_MAX}" "${java_version_max_hr}")"
-		fi
-
-		# log exit cause
-		stub_logger "[EXIT 3] ${MSG_NO_SUITABLE_JAVA_EXPANDED}"
-
-		# display error message with AppleScript
-		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_NO_SUITABLE_JAVA_EXPANDED}\n${MSG_NO_SUITABLE_JAVA_CHECK}\" with title \"${CFBundleName}\"  buttons {\" OK \", \"${MSG_VISIT_JAVA_DOT_COM}\"} default button \"${MSG_VISIT_JAVA_DOT_COM}\" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" \
-				-e "set response to button returned of the result" \
-				-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"http://java.com\""
-		# exit with error
-		exit 3
-
-	else
-		# log exit cause
-		stub_logger "[EXIT 1] ${MSG_ERROR_LAUNCHING}"
-		# display error message with AppleScript
-		osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_INSTALL_JAVA}\" with title \"${CFBundleName}\" buttons {\"${MSG_LATER}\", \"${MSG_VISIT_JAVA_DOT_COM}\"} default button \"${MSG_VISIT_JAVA_DOT_COM}\" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" \
-					-e "set response to button returned of the result" \
-					-e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"http://java.com\""
-		# exit with error
-		exit 1
-	fi
-fi
-
-
-
-# MainClass check
-############################################
-
-if [ -z "${JVMMainClass}" ]; then
-	# log exit cause
-	stub_logger "[EXIT 2] ${MSG_MISSING_MAINCLASS}"
-	# display error message with AppleScript
-	osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_MISSING_MAINCLASS}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)"
-	# exit with error
-	exit 2
-fi
-
-
-
-# execute $JAVACMD and do some preparation
-############################################
-
-# enable drag&drop to the dock icon
-export CFProcessPath="$0"
-
-# remove Apples ProcessSerialNumber from passthru arguments (#39)
-if [[ "$*" == -psn* ]] ; then
-	ArgsPassthru=()
-else
-	ArgsPassthru=("$@")
-fi
-
-# change to Working Directory based upon Apple/Oracle Plist info
-cd "${WorkingDirectory}" || exit 13
-stub_logger "[WorkingDirectory] ${WorkingDirectory}"
-
-# execute Java and set
-# - classpath
-# - splash image
-# - dock icon
-# - app name
-# - JVM options / properties (-D)
-# - JVM default options (-X)
-# - main class
-# - main class arguments
-# - passthrough arguments from Terminal or Drag'n'Drop to Finder icon
-stub_logger "[Exec] \"$JAVACMD\" -cp \"${JVMClassPath}\" -splash:\"${ResourcesFolder}/${JVMSplashFile}\" -Xdock:icon=\"${ResourcesFolder}/${CFBundleIconFile}\" -Xdock:name=\"${CFBundleName}\" ${JVMOptionsArr:+$(printf "'%s' " "${JVMOptionsArr[@]}") }${JVMDefaultOptions:+$JVMDefaultOptions }${JVMMainClass}${MainArgsArr:+ $(printf "'%s' " "${MainArgsArr[@]}")}${ArgsPassthru:+ $(printf "'%s' " "${ArgsPassthru[@]}")}"
-exec "${JAVACMD}" \
-		-cp "${JVMClassPath}" \
-		-splash:"${ResourcesFolder}/${JVMSplashFile}" \
-		-Xdock:icon="${ResourcesFolder}/${CFBundleIconFile}" \
-		-Xdock:name="${CFBundleName}" \
-		${JVMOptions:+"${JVMOptions[@]}" }\
-		${JVMDefaultOptions:+$JVMDefaultOptions }\
-		"${JVMMainClass}"\
-		${MainArgsArr:+ "${MainArgsArr[@]}"}\
-		${ArgsPassthru:+ "${ArgsPassthru[@]}"}
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/app/BEASTVersion2.java beast2-mcmc-2.6.7+dfsg/src/beast/app/BEASTVersion2.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/app/BEASTVersion2.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/app/BEASTVersion2.java	2022-04-04 07:18:36.000000000 +0000
@@ -9,11 +9,11 @@
     /**
      * Version string: assumed to be in format x.x.x
      */
-    private static final String VERSION = "2.6.6";
+    private static final String VERSION = "2.6.7";
 
-    private static final String DATE_STRING = "2002-2021";
+    private static final String DATE_STRING = "2002-2022";
 
-    private static final boolean IS_PRERELEASE = false;
+    private static final boolean IS_PRERELEASE = true;
 //
 //    private static final String BEAST2_WEBPAGE = "http://beast2.org/";
 //    
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/app/BEASTVersion.java beast2-mcmc-2.6.7+dfsg/src/beast/app/BEASTVersion.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/app/BEASTVersion.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/app/BEASTVersion.java	2022-04-04 07:18:36.000000000 +0000
@@ -19,11 +19,11 @@
     /**
      * Version string: assumed to be in format x.x.x
      */
-    private static final String VERSION = "2.6.6";
+    private static final String VERSION = "2.6.7";
 
-    private static final String DATE_STRING = "2002-2021";
+    private static final String DATE_STRING = "2002-2022";
 
-    private static final boolean IS_PRERELEASE = false;
+    private static final boolean IS_PRERELEASE = true;
 
     private static final String BEAST2_WEBPAGE = "http://beast2.org/";
     
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/app/beauti/BeautiAlignmentProvider.java beast2-mcmc-2.6.7+dfsg/src/beast/app/beauti/BeautiAlignmentProvider.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/app/beauti/BeautiAlignmentProvider.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/app/beauti/BeautiAlignmentProvider.java	2022-04-04 07:18:36.000000000 +0000
@@ -9,14 +9,7 @@
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 
 import javax.swing.JComboBox;
 import javax.swing.JOptionPane;
@@ -558,16 +551,50 @@
 			        if (mayBeAminoacid) {
 			        	switch (this.datatype) {
 				        	case userdefined:
-				        		// make user choose 
-					        	JComboBox<String> jcb = new JComboBox<>(new String[]{"aminoacid", "nucleotide", "all are aminoacid", "all are nucleotide"});
-					        	jcb.setEditable(true);
+				        		// make user choose
+								TreeMap<String, DataType> allTypes = Alignment.getTypes();
+								String[] dataNames = new String[allTypes.keySet().size() + 2];
+								dataNames[0] = "aminoacid";
+								dataNames[1] = "nucleotide";
+								dataNames[2] = "all are aminoacid";
+								dataNames[3] = "all are nucleotide";
+								int i = 4;
+								for (String key: allTypes.keySet()) {
+									if (!key.equals("nucleotide") && !key.equals("aminoacid")) {
+										dataNames[i] = key;
+										i++;
+									}
+								}
+								JComboBox<String> jcb = new JComboBox<>(dataNames);
+								jcb.setEditable(true);
 					        	jcb.setSelectedItem(datatype);
 					        	JOptionPane.showMessageDialog(null, jcb, "Choose the datatype of alignment " + alignment.getID(), JOptionPane.QUESTION_MESSAGE);
-					        	switch ((String) jcb.getSelectedItem()) {
-						        	case "aminoacid": datatype = "aminoacid"; totalCount = 20; break;
-						        	case "nucleotide": datatype = "nucleotide"; totalCount = 4; break;
-						        	case "all are aminoacid": datatype = "aminoacid"; this.datatype = dtype.aminoacid; totalCount = 20; break;
-						        	case "all are nucleotide": datatype = "nucleotide"; this.datatype = dtype.nucleotide; totalCount = 4; break;
+					        	// match selected data type
+					        	String selectedType = (String) jcb.getSelectedItem();
+					        	switch (selectedType) {
+						        	case "aminoacid":
+						        		datatype = "aminoacid";
+						        		totalCount = 20;
+						        		break;
+						        	case "nucleotide":
+						        		datatype = "nucleotide";
+						        		totalCount = 4;
+						        		break;
+						        	case "all are aminoacid":
+						        		datatype = "aminoacid";
+						        		this.datatype = dtype.aminoacid;
+						        		totalCount = 20;
+						        		break;
+						        	case "all are nucleotide":
+						        		datatype = "nucleotide";
+						        		this.datatype = dtype.nucleotide;
+						        		totalCount = 4;
+						        		break;
+									default:
+										// catch all for other data types
+										datatype = selectedType;
+										totalCount = allTypes.get(selectedType).getStateCount();
+										break;
 					        	}
 					        	break;
 				        	case aminoacid:
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/app/beauti/BeautiDoc.java beast2-mcmc-2.6.7+dfsg/src/beast/app/beauti/BeautiDoc.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/app/beauti/BeautiDoc.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/app/beauti/BeautiDoc.java	2022-04-04 07:18:36.000000000 +0000
@@ -71,6 +71,7 @@
 import beast.evolution.substitutionmodel.SubstitutionModel;
 import beast.evolution.tree.TraitSet;
 import beast.evolution.tree.Tree;
+import beast.evolution.tree.TreeInterface;
 import beast.math.distributions.MRCAPrior;
 import beast.math.distributions.Normal;
 import beast.math.distributions.ParametricDistribution;
@@ -166,7 +167,7 @@
     InputEditorFactory inputEditorFactory;
 
     /** used to capture Stdout and Stderr **/
-    static ByteArrayOutputStream baos = null;
+    static public ByteArrayOutputStream baos = null;
 
 
     public InputEditorFactory getInputEditorFactory() {
@@ -414,7 +415,7 @@
 //      fireDocHasChanged();
     }
 
-    void fireDocHasChanged()  {
+    public void fireDocHasChanged()  {
         for (BeautiDocListener listener : listeners) {
             try {
                 listener.docHasChanged();
@@ -976,7 +977,7 @@
      *
      * @ *
      */
-    void connectModel()  {
+    public void connectModel()  {
         scrubAll(true, true);
     }
 
@@ -1331,16 +1332,18 @@
         }
 
         BEASTInterface likelihood = pluginmap.get("likelihood");
+        Set<TreeInterface> treesSeen = new HashSet<>();
         if (likelihood instanceof CompoundDistribution) {
             int i = 0;
             RealParameter firstClock = null;
             for (Distribution distr : ((CompoundDistribution) likelihood).pDistributions.get()) {
                 if (distr instanceof GenericTreeLikelihood) {
-                    GenericTreeLikelihood treeLikelihood = (GenericTreeLikelihood) distr;
+                    GenericTreeLikelihood treeLikelihood = (GenericTreeLikelihood) distr;                    
+                    TreeInterface currentTree = treeLikelihood.treeInput.get();
                     boolean needsEstimation = needsEstimationBySPTree;
                     if (i > 0) {
                         BranchRateModel.Base model = treeLikelihood.branchRateModelInput.get();
-                        needsEstimation = (model.meanRateInput.get() != firstClock) || firstClock.isEstimatedInput.get();
+                        needsEstimation = (model.meanRateInput.get() != firstClock && treesSeen.contains(currentTree)) || firstClock.isEstimatedInput.get();
                     } else {
                         // TODO: this might not be a valid type conversion from TreeInterface to Tree
                         Tree tree = (Tree) treeLikelihood.treeInput.get();
@@ -1366,6 +1369,7 @@
                             firstClock = clockRate;
                         }
                     }
+                    treesSeen.add(currentTree);
                     i++;
                 }
             }
@@ -2021,7 +2025,7 @@
         return deepCopy;
     } // deepCopyPlugin
 
-    private static BEASTInterface getCopyValue(BEASTInterface value, Map<String, BEASTInterface> copySet, PartitionContext oldContext, PartitionContext partitionContext, BeautiDoc doc) {
+    public static BEASTInterface getCopyValue(BEASTInterface value, Map<String, BEASTInterface> copySet, PartitionContext oldContext, PartitionContext partitionContext, BeautiDoc doc) {
         if (copySet.containsKey(value.getID())) {
             value = copySet.get(value.getID());
             return value;
@@ -2247,7 +2251,7 @@
 
 
     // methods for dealing with linking
-    void determineLinks() {
+    public void determineLinks() {
         if (!allowLinking) {
             return;
         }
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/app/beauti/GuessPatternDialog.java beast2-mcmc-2.6.7+dfsg/src/beast/app/beauti/GuessPatternDialog.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/app/beauti/GuessPatternDialog.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/app/beauti/GuessPatternDialog.java	2022-04-04 07:18:36.000000000 +0000
@@ -571,8 +571,13 @@
                 while (fin.ready()) {
                     String[] strArray = fin.readLine().trim().split("\t");
                     // only add entries that are non-empty
-                    if (strArray.length == 2) {
-                        traitMap.put(strArray[0], strArray[1]);
+                    if (strArray.length >= 2) {
+                    	String str = strArray[1];
+                    	int k = 2;
+                    	while (k < strArray.length) {
+                    		str += "\t" + strArray[k++];
+                    	}
+                        traitMap.put(strArray[0], str);
                     }
                 }
                 fin.close();
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/app/seqgen/SimulatedAlignment.java beast2-mcmc-2.6.7+dfsg/src/beast/app/seqgen/SimulatedAlignment.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/app/seqgen/SimulatedAlignment.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/app/seqgen/SimulatedAlignment.java	2022-04-04 07:18:36.000000000 +0000
@@ -126,7 +126,24 @@
 //    		}
 //			seq.append(seq[m_sequenceLength-1] + "");
 //    	}
-        String taxon = m_data.get().getTaxaNames().get(node.getNr());
+        //String taxon = m_data.get().getTaxaNames().get(node.getNr());
+        
+        
+        
+        // Find taxon with same name if tree is labelled
+        int taxonNum = node.getNr();
+        if (node.getID() != null && !node.getID().isEmpty()) {
+	        for (int i = 0; i < m_data.get().getTaxaNames().size(); i ++) {
+	        	if (m_data.get().getTaxaNames().get(i).equals(node.getID())) {
+	        		taxonNum=i;
+	        		break;
+	        	}
+	        }
+        }
+        
+        String taxon = m_data.get().getTaxaNames().get(taxonNum);
+        
+        
         return new Sequence(taxon, seqString);
     } // intArray2Sequence
 
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/app/treeannotator/TreeAnnotator.java beast2-mcmc-2.6.7+dfsg/src/beast/app/treeannotator/TreeAnnotator.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/app/treeannotator/TreeAnnotator.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/app/treeannotator/TreeAnnotator.java	2022-04-04 07:18:36.000000000 +0000
@@ -1402,7 +1402,7 @@
                 new Arguments.Option[]{
                         //new Arguments.StringOption("target", new String[] { "maxclade", "maxtree" }, false, "an option of 'maxclade' or 'maxtree'"),
                         new Arguments.StringOption("heights", new String[]{"keep", "median", "mean", "ca"}, false,
-                                "an option of 'keep' (default), 'median', 'mean' or 'ca'"),
+                                "one of 'ca' (default), 'median', 'mean' or 'keep'"),
                         new Arguments.IntegerOption("burnin", 0, 99, "the percentage of states to be considered as 'burn-in'"),
                         // allow -b as burnin option, just like other apps
                         new Arguments.IntegerOption("b", 0, 99, "the percentage of states to be considered as 'burn-in'"),
@@ -1454,11 +1454,15 @@
                 heights = HeightsSummary.MEAN_HEIGHTS;
             } else if (value.equalsIgnoreCase("median")) {
                 heights = HeightsSummary.MEDIAN_HEIGHTS;
-            } else if (value.equalsIgnoreCase("ca")) {
-                heights = HeightsSummary.CA_HEIGHTS;
-                Log.info.println("Please cite: Heled and Bouckaert: Looking for trees in the forest:\n" +
-                                        "summary tree from posterior samples. BMC Evolutionary Biology 2013 13:221.");
+            } else if (value.equalsIgnoreCase("keep")) {
+                heights = HeightsSummary.KEEP_HEIGHTS;
             }
+            // Otherwise, use CA heights
+        }
+
+        if (heights == HeightsSummary.CA_HEIGHTS) {
+            Log.info.println("Please cite: Heled and Bouckaert: Looking for trees in the forest:\n" +
+                    "summary tree from posterior samples. BMC Evolutionary Biology 2013 13:221.");
         }
 
         int burnin = -1;
@@ -1503,8 +1507,7 @@
                 inputFileName = args2[0];
                 break;
             default: {
-                Log.err.println("Unknown option: " + args2[2]);
-                Log.err.println();
+                Log.err.println("\nCommand not understood.\n");
                 printUsage(arguments);
                 System.exit(1);
             }
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/core/Logger.java beast2-mcmc-2.6.7+dfsg/src/beast/core/Logger.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/core/Logger.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/core/Logger.java	2022-04-04 07:18:36.000000000 +0000
@@ -70,7 +70,9 @@
     final public Input<LOGMODE> modeInput = new Input<>("mode", "logging mode, one of " + Arrays.toString(LOGMODE.values()), LOGMODE.autodetect, LOGMODE.values());
     final public Input<SORTMODE> sortModeInput = new Input<>("sort", "sort items to be logged, one of " + Arrays.toString(SORTMODE.values()), SORTMODE.none, SORTMODE.values());
     final public Input<Boolean> sanitiseHeadersInput = new Input<>("sanitiseHeaders", "whether to remove any clutter introduced by Beauti" , false);
+    final public Input<Boolean> convertToASCIIInput = new Input<>("ascii", "whether to convert the log output to ASCII" , true);
 
+    
     final public Input<List<BEASTObject>> loggersInput = new Input<>("log",
             "Element in a log. This can be any plug in that is Loggable.",
             new ArrayList<>(), Validate.REQUIRED, Loggable.class);
@@ -658,7 +660,11 @@
         // Acquire log string and trim excess tab
         String logContent;
         try {
-            logContent = baos.toString("ASCII").trim();
+        	
+        	// Convert to ASCII?
+        	if (convertToASCIIInput.get()) logContent = baos.toString("ASCII").trim();
+        	else logContent = baos.toString().trim();
+        	
         } catch (UnsupportedEncodingException e) {
             throw new RuntimeException("ASCII string encoding not supported: required for logging!");
         }
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/evolution/alignment/Alignment.java beast2-mcmc-2.6.7+dfsg/src/beast/evolution/alignment/Alignment.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/evolution/alignment/Alignment.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/evolution/alignment/Alignment.java	2022-04-04 07:18:36.000000000 +0000
@@ -56,7 +56,7 @@
     /**
      * list of data type descriptions, obtained from DataType classes *
      */
-    static TreeMap<String, DataType> types = new TreeMap<>();
+    static TreeMap<String, DataType> types = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
 
     static {
         findDataTypes();
@@ -86,6 +86,10 @@
         return types.get(name);
     }
 
+    static public TreeMap<String, DataType> getTypes() {
+        return types;
+    }
+
     final public Input<List<Sequence>> sequenceInput =
             new Input<>("sequence", "sequence and meta data for particular taxon", new ArrayList<>(), Validate.OPTIONAL);
 
@@ -272,7 +276,7 @@
             DataType dataType;
             try {
                 dataType = (DataType) BEASTClassLoader.forName(dataTypeName).newInstance();
-                if (dataTypeInput.get().equals(dataType.getTypeDescription())) {
+                if (dataTypeInput.get().equalsIgnoreCase(dataType.getTypeDescription())) {
                     m_dataType = dataType;
                     break;
                 }
@@ -374,6 +378,23 @@
             excludedPatterns = new HashSet<>();
             for (int i = from; i < to; i += every) {
                 int patternIndex_ = patternIndex[i];
+                
+                if (patternWeight[patternIndex_] > 1) {
+                	// when the pattern weight is 2 or larger, perhaps a site that is ascertained for
+                	// accidentally made it into the alignment. Regardless, its contribution to the
+                	// likelihood will be ignored by setting the weight to zero in the line after this
+                	// sanity check, so warn the user about this possibility.
+                	if (to-from == 1) {
+                		int n = patternWeight[patternIndex_] - 1;
+                		Log.warning("WARNING: found " + (n==1?"a site": n+ " sites") + " in the alignment (" + getID() + ") "
+                			+ "that are equal to the ascertainment site. These sites will be ignored in the likelihood "
+                			+ "calculation.");
+                	} else {
+                    	Log.warning("WARNING: found multiple entries for a site that occurs multiple times and is ascertained "
+                    		+ "for. This may indicate some sites should be removed. Regardless, these sites will be ignored in "
+                    		+ "the likelihood calculation.");
+                	}
+                }
                 // reduce weight, so it does not confuse the tree likelihood
                 patternWeight[patternIndex_] = 0;
                 excludedPatterns.add(patternIndex_);
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/evolution/branchratemodel/RateStatistic.java beast2-mcmc-2.6.7+dfsg/src/beast/evolution/branchratemodel/RateStatistic.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/evolution/branchratemodel/RateStatistic.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/evolution/branchratemodel/RateStatistic.java	2022-04-04 07:18:36.000000000 +0000
@@ -48,7 +48,7 @@
 	
     final public Input<GenericTreeLikelihood> likelihoodInput = new Input<>("treeLikelihood", "TreeLikelihood containing branch rate model that provides rates for a tree");
     final public Input<BranchRateModel> branchRateModelInput = new Input<>("branchratemodel", "model that provides rates for a tree", Validate.XOR, likelihoodInput);
-    final public Input<Tree> treeInput = new Input<>("tree", "tree for which the rates apply");
+    final public Input<Tree> treeInput = new Input<>("tree", "tree for which the rates apply", Validate.REQUIRED);
     final public Input<Boolean> internalInput = new Input<>("internal", "consider internal nodes, default true", true);
     final public Input<Boolean> externalInput = new Input<>("external", "consider external nodes, default true", true);
 
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/evolution/operators/TipDatesRandomWalker.java beast2-mcmc-2.6.7+dfsg/src/beast/evolution/operators/TipDatesRandomWalker.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/evolution/operators/TipDatesRandomWalker.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/evolution/operators/TipDatesRandomWalker.java	2022-04-04 07:18:36.000000000 +0000
@@ -84,7 +84,12 @@
 
         if (newValue > node.getParent().getHeight()) { // || newValue < 0.0) {
             if (reflectValue) {
-                newValue = reflectValue(newValue, 0.0, node.getParent().getHeight());
+            	double h = node.getParent().getHeight();
+            	// tips heights may become less than 0, so their parents can have height < 0 as well
+            	// https://github.com/CompEvol/beast2/issues/995
+            	// so the range (0, h) may become empty
+            	// therefore, set lower bound on range to min(0.0, node height) 
+                newValue = reflectValue(newValue, Math.min(0.0, node.getHeight()), h);
             } else {
                 return Double.NEGATIVE_INFINITY;
             }
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/evolution/tree/RandomTree.java beast2-mcmc-2.6.7+dfsg/src/beast/evolution/tree/RandomTree.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/evolution/tree/RandomTree.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/evolution/tree/RandomTree.java	2022-04-04 07:18:36.000000000 +0000
@@ -234,8 +234,8 @@
 	        			beastObjects.get(i).initAndValidate();
 	        		}
 	                try {
-	                	double tLow = distr.inverseCumulativeProbability(0.0) + distr.offsetInput.get();
-	                	double tHi = distr.inverseCumulativeProbability(1.0) + distr.offsetInput.get();
+	                	double tLow = distr.inverseCumulativeProbability(0.0);
+	                	double tHi = distr.inverseCumulativeProbability(1.0);
 						bounds.lower = getDate(tLow);
 		                bounds.upper = getDate(tHi);
 		                if (bounds.lower > bounds.upper && tLow < tHi) {
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/math/distributions/Prior.java beast2-mcmc-2.6.7+dfsg/src/beast/math/distributions/Prior.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/math/distributions/Prior.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/math/distributions/Prior.java	2022-04-04 07:18:36.000000000 +0000
@@ -87,29 +87,45 @@
         try {
             newx = dist.sample(1)[0];
 
-            if (newx.length == x.getDimension()) {            	
-	            if (x instanceof RealParameter) {
-	                for (int i = 0; i < newx.length; i++) {
-	                    ((RealParameter) x).setValue(i, newx[i]);
-	                }
-	            } else if (x instanceof IntegerParameter) {
-	                for (int i = 0; i < newx.length; i++) {
-	                    ((IntegerParameter) x).setValue(i, (int)Math.round(newx[i]));
-	                }
-	            }
-            } else if (newx.length == 1) {
-            	// assume it is a multi dimensional distribution with iid components
-            	for (int k = 0; k < x.getDimension(); k++) {
-		            if (x instanceof RealParameter) {
-		                ((RealParameter) x).setValue(k, newx[0]);
-		            } else if (x instanceof IntegerParameter) {
-		                ((IntegerParameter) x).setValue(k, (int)Math.round(newx[0]));
-		            }
-		            if (k < x.getDimension()-1) {
-		            	newx = dist.sample(1)[0];
-		            }
-            	}
+            if (newx.length == x.getDimension()) {              
+                if (x instanceof RealParameter) {
+                    RealParameter p = (RealParameter) x;
+                    for (int i = 0; i < newx.length; i++) {
+                            while (p.getLower() > newx[i] || p.getUpper() < newx[i]) {
+                                    newx = dist.sample(1)[0];
+                            }
+                        ((RealParameter) x).setValue(i, newx[i]);
+                    }
+                } else if (x instanceof IntegerParameter) {
+                    IntegerParameter p = (IntegerParameter) x;
+                    for (int i = 0; i < newx.length; i++) {
+                            while (p.getLower() > newx[i] || p.getUpper() < newx[i]) {
+                                    newx = dist.sample(1)[0];
+                            }
+                        p.setValue(i, (int)Math.round(newx[i]));
+                    }
+                }
+        } else if (newx.length == 1) {
+            // assume it is a multi dimensional distribution with iid components
+            for (int k = 0; k < x.getDimension(); k++) {
+                        if (x instanceof RealParameter) {
+                            RealParameter p = (RealParameter) x;
+                            while (p.getLower() > newx[0] || p.getUpper() < newx[0]) {
+                                    newx = dist.sample(1)[0];
+                            }
+                            p.setValue(k, newx[0]);
+                        } else if (x instanceof IntegerParameter) {
+                            IntegerParameter p = (IntegerParameter) x;
+                            while (p.getLower() > newx[0] || p.getUpper() < newx[0]) {
+                                    newx = dist.sample(1)[0];
+                            }
+                            p.setValue(k, (int)Math.round(newx[0]));
+                        }
+                        if (k < x.getDimension()-1) {
+                            newx = dist.sample(1)[0];
+                        }
             }
+        }
         } catch (MathException e) {
             e.printStackTrace();
             throw new RuntimeException("Failed to sample!");
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/util/NexusParser.java beast2-mcmc-2.6.7+dfsg/src/beast/util/NexusParser.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/util/NexusParser.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/util/NexusParser.java	2022-04-04 07:18:36.000000000 +0000
@@ -760,7 +760,9 @@
                     // generic data type look up if nothing else works
                     DataType dataType = Alignment.getDataTypeByName(dataTypeName);
                     if (dataType != null) {
-                        alignment.dataTypeInput.setValue(dataTypeName, alignment);
+                        // robustly set data type for names with upper and lower case
+                        String dataTypeNameRobust = Alignment.getDataTypeByName(dataTypeName).getTypeDescription();
+                        alignment.dataTypeInput.setValue(dataTypeNameRobust, alignment);
                         totalCount = dataType.getStateCount();
                     }  else {
                         // set to integer as last resort
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/util/XMLParser.java beast2-mcmc-2.6.7+dfsg/src/beast/util/XMLParser.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/util/XMLParser.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/util/XMLParser.java	2022-04-04 07:18:36.000000000 +0000
@@ -963,7 +963,7 @@
 		} catch (InstantiationException e) {
 			// we only get here when the class exists, but cannot be
 			// created for instance because it is abstract
-            String msg = "Class " + clazzName + " exists but cannot to be instantiated.\n" +
+            String msg = "Class " + clazzName + " exists but cannot be instantiated.\n" +
                     "Please check if the class has the zero-argument constructor.";
 			throw new XMLParserException(node, msg, 1006);
 		} catch (ClassNotFoundException e) {
diff -Nru beast2-mcmc-2.6.6+dfsg/src/beast/util/XMLProducer.java beast2-mcmc-2.6.7+dfsg/src/beast/util/XMLProducer.java
--- beast2-mcmc-2.6.6+dfsg/src/beast/util/XMLProducer.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/beast/util/XMLProducer.java	2022-04-04 07:18:36.000000000 +0000
@@ -157,6 +157,25 @@
             xml = dedupName(xml);
             xml = sortTags(xml);
             
+            // remove double newlines introduced by XSL transformation
+            StringBuilder b = new StringBuilder();
+            for (int i = 0; i < xml.length(); i++) {
+            	char c = xml.charAt(i);
+            	if (c == '\n') {
+            		int j = 0;
+            		while (i < xml.length()-1 && xml.charAt(i+1) == ' ') {
+            			i++;
+            			j++;
+            		}
+            		if (i < xml.length()-1 && xml.charAt(i+1) == '\n') {
+            			i++;
+            		} else {
+            			i = i - j;
+            		}
+            	}
+            	b.append(c);
+            }
+            xml = b.toString();
 
             //insert newlines in alignments
             int k = xml.indexOf("<data ");
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -48,9 +48,9 @@
 
         assertThat(f).isNotNull();
         printBeautiState(f);
-        assertStateEquals("Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "Tree.t:coding", "birthRate.t:coding", "Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos");
-        assertOperatorsEqual("StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "strictClockUpDownOperator.c:1stpos", "strictClockUpDownOperator.c:2ndpos", "strictClockUpDownOperator.c:noncoding");
-        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:coding", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos");
+        assertStateEquals("Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:2ndpos", "birthRate.t:2ndpos", "Tree.t:1stpos", "birthRate.t:1stpos", "Tree.t:coding", "birthRate.t:coding", "Tree.t:3rdpos", "birthRate.t:3rdpos");
+        assertOperatorsEqual("YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos");
+        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:coding", "YuleBirthRatePrior.t:3rdpos");
 
 
         //1. Delete "coding" partition as it covers the same sites as the 1stpos, 2ndpos and 3rdpos partitions.
@@ -65,9 +65,9 @@
                 "[1stpos, primate-mtDNA, 12, 231, nucleotide, 1stpos, 1stpos, 1stpos, false]*" +
                 "[2ndpos, primate-mtDNA, 12, 231, nucleotide, 2ndpos, 2ndpos, 2ndpos, false]*" +
                 "[3rdpos, primate-mtDNA, 12, 231, nucleotide, 3rdpos, 3rdpos, 3rdpos, false]");
-        assertStateEquals("Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos");
-        assertOperatorsEqual("YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:3rdpos", "strictClockUpDownOperator.c:2ndpos", "strictClockUpDownOperator.c:1stpos");
-        assertPriorsEqual("YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleModel.t:noncoding", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:3rdpos", "YuleBirthRatePrior.t:noncoding", "ClockPrior.c:1stpos", "ClockPrior.c:2ndpos", "ClockPrior.c:3rdpos");
+        assertStateEquals("Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:3rdpos", "birthRate.t:3rdpos", "Tree.t:1stpos", "birthRate.t:1stpos", "Tree.t:2ndpos", "birthRate.t:2ndpos");
+        assertOperatorsEqual("YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos");
+        assertPriorsEqual("YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleModel.t:noncoding", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:3rdpos", "YuleBirthRatePrior.t:noncoding");
 
 
         //2a. Link trees...
@@ -317,9 +317,9 @@
 
             assertThat(f).isNotNull();
             printBeautiState(f);
-            assertStateEquals("Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "Tree.t:coding", "birthRate.t:coding", "Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos");
-            assertOperatorsEqual("StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "strictClockUpDownOperator.c:1stpos", "strictClockUpDownOperator.c:2ndpos", "strictClockUpDownOperator.c:noncoding");
-            assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:coding", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos");
+            assertStateEquals("Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:2ndpos", "birthRate.t:2ndpos", "Tree.t:1stpos", "birthRate.t:1stpos", "Tree.t:coding", "birthRate.t:coding", "Tree.t:3rdpos", "birthRate.t:3rdpos");
+            assertOperatorsEqual("YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos");
+            assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:coding", "YuleBirthRatePrior.t:3rdpos");
 
 
             //1. Delete "coding" partition as it covers the same sites as the 1stpos, 2ndpos and 3rdpos partitions.
@@ -334,9 +334,9 @@
                     "[1stpos, primate-mtDNA, 12, 231, nucleotide, 1stpos, 1stpos, 1stpos, false]*" +
                     "[2ndpos, primate-mtDNA, 12, 231, nucleotide, 2ndpos, 2ndpos, 2ndpos, false]*" +
                     "[3rdpos, primate-mtDNA, 12, 231, nucleotide, 3rdpos, 3rdpos, 3rdpos, false]");
-            assertStateEquals("Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos");
-            assertOperatorsEqual("YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:3rdpos", "strictClockUpDownOperator.c:2ndpos", "strictClockUpDownOperator.c:1stpos");
-            assertPriorsEqual("YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleModel.t:noncoding", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:3rdpos", "YuleBirthRatePrior.t:noncoding", "ClockPrior.c:1stpos", "ClockPrior.c:2ndpos", "ClockPrior.c:3rdpos");
+            assertStateEquals("Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:3rdpos", "birthRate.t:3rdpos", "Tree.t:1stpos", "birthRate.t:1stpos", "Tree.t:2ndpos", "birthRate.t:2ndpos");
+            assertOperatorsEqual("YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos");
+            assertPriorsEqual("YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleModel.t:noncoding", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:3rdpos", "YuleBirthRatePrior.t:noncoding");
 
             //2a. Link trees...
             warning("2a. Link trees...");
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/app/beauti/CloneTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/app/beauti/CloneTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/app/beauti/CloneTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/app/beauti/CloneTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -11,6 +11,7 @@
 import org.fest.swing.fixture.JComboBoxFixture;
 import org.fest.swing.fixture.JListFixture;
 import org.fest.swing.fixture.JTabbedPaneFixture;
+import org.fest.swing.fixture.JTableFixture;
 import org.fest.swing.fixture.JTextComponentFixture;
 import org.junit.Test;
 
@@ -41,10 +42,10 @@
         JCheckBoxFixture shapeIsEstimated = beautiFrame.checkBox("shape.isEstimated");
         shapeIsEstimated.check();
         printBeautiState(f);
-        assertStateEquals("Tree.t:coding", "birthRate.t:coding", "Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "kappa.s:coding", "gammaShape.s:coding", "freqParameter.s:coding");
-        assertOperatorsEqual("YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "strictClockUpDownOperator.c:noncoding", "StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "FrequenciesExchanger.s:coding");
-        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleBirthRatePrior.t:coding", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "FrequenciesPrior.s:coding");
-        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "clockRate.c:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "kappa.s:coding", "gammaShape.s:coding", "freqParameter.s:coding");
+        assertStateEquals("Tree.t:coding", "birthRate.t:coding", "Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:3rdpos", "birthRate.t:3rdpos", "Tree.t:1stpos", "birthRate.t:1stpos", "Tree.t:2ndpos", "birthRate.t:2ndpos", "kappa.s:coding", "gammaShape.s:coding", "freqParameter.s:coding");
+        assertOperatorsEqual("YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "FrequenciesExchanger.s:coding");
+        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleBirthRatePrior.t:coding", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:3rdpos", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:2ndpos", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "FrequenciesPrior.s:coding");
+        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "kappa.s:coding", "gammaShape.s:coding", "freqParameter.s:coding");
 
         //2. select all models, clone from first model
         warning("2. select all models, clone from first model");
@@ -54,10 +55,10 @@
         JButtonFixture cloneButton = beautiFrame.button("ok");
         cloneButton.click();
         printBeautiState(f);
-        assertStateEquals("Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "Tree.t:coding", "birthRate.t:coding", "Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:noncoding", "gammaShape.s:1stpos", "kappa.s:1stpos", "gammaShape.s:2ndpos", "kappa.s:2ndpos", "gammaShape.s:3rdpos", "kappa.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:noncoding", "freqParameter.s:coding");
-        assertOperatorsEqual("StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "strictClockUpDownOperator.c:noncoding", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "gammaShapeScaler.s:noncoding", "KappaScaler.s:noncoding", "gammaShapeScaler.s:1stpos", "KappaScaler.s:1stpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:3rdpos", "KappaScaler.s:3rdpos", "FrequenciesExchanger.s:1stpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:noncoding", "FrequenciesExchanger.s:coding");
-        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:coding", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "GammaShapePrior.s:noncoding", "KappaPrior.s:noncoding", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos", "FrequenciesPrior.s:coding", "FrequenciesPrior.s:noncoding", "FrequenciesPrior.s:1stpos", "FrequenciesPrior.s:2ndpos", "FrequenciesPrior.s:3rdpos");
-        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "clockRate.c:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:noncoding", "gammaShape.s:1stpos", "kappa.s:1stpos", "gammaShape.s:2ndpos", "kappa.s:2ndpos", "gammaShape.s:3rdpos", "kappa.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:noncoding", "freqParameter.s:coding");
+        assertStateEquals("Tree.t:1stpos", "birthRate.t:1stpos", "Tree.t:coding", "birthRate.t:coding", "Tree.t:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "birthRate.t:noncoding", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:noncoding", "gammaShape.s:1stpos", "kappa.s:1stpos", "gammaShape.s:2ndpos", "kappa.s:2ndpos", "gammaShape.s:3rdpos", "kappa.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:noncoding", "freqParameter.s:coding");
+        assertOperatorsEqual("YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "gammaShapeScaler.s:noncoding", "KappaScaler.s:noncoding", "gammaShapeScaler.s:1stpos", "KappaScaler.s:1stpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:3rdpos", "KappaScaler.s:3rdpos", "FrequenciesExchanger.s:1stpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:noncoding", "FrequenciesExchanger.s:coding");
+        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:coding", "YuleBirthRatePrior.t:3rdpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:noncoding", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "GammaShapePrior.s:noncoding", "KappaPrior.s:noncoding", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos", "FrequenciesPrior.s:coding", "FrequenciesPrior.s:noncoding", "FrequenciesPrior.s:1stpos", "FrequenciesPrior.s:2ndpos", "FrequenciesPrior.s:3rdpos");
+        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:noncoding", "gammaShape.s:1stpos", "kappa.s:1stpos", "gammaShape.s:2ndpos", "kappa.s:2ndpos", "gammaShape.s:3rdpos", "kappa.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:noncoding", "freqParameter.s:coding");
 
         //3. set second model back to JC
         warning("3. select all models, clone from first model");
@@ -65,19 +66,19 @@
         beautiFrame.comboBox("substModel").selectItem("JC69");
         beautiFrame.textBox("gammaCategoryCount").setText("6");
         printBeautiState(f);
-        assertStateEquals("Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
-        assertOperatorsEqual("StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "strictClockUpDownOperator.c:noncoding", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "gammaShapeScaler.s:noncoding", "KappaScaler.s:1stpos", "gammaShapeScaler.s:1stpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:3rdpos", "gammaShapeScaler.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:1stpos", "FrequenciesExchanger.s:coding");
-        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:coding", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "GammaShapePrior.s:noncoding", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos", "FrequenciesPrior.s:coding", "FrequenciesPrior.s:1stpos", "FrequenciesPrior.s:2ndpos", "FrequenciesPrior.s:3rdpos");
-        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "clockRate.c:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
+        assertStateEquals("Tree.t:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
+        assertOperatorsEqual("YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "gammaShapeScaler.s:noncoding", "KappaScaler.s:1stpos", "gammaShapeScaler.s:1stpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:3rdpos", "gammaShapeScaler.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:1stpos", "FrequenciesExchanger.s:coding");
+        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleBirthRatePrior.t:3rdpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:coding", "YuleBirthRatePrior.t:1stpos", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "GammaShapePrior.s:noncoding", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos", "FrequenciesPrior.s:coding", "FrequenciesPrior.s:1stpos", "FrequenciesPrior.s:2ndpos", "FrequenciesPrior.s:3rdpos");
+        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
 
         // set category count back to 1
         beautiFrame.checkBox("shape.isEstimated").uncheck();
         beautiFrame.textBox("gammaCategoryCount").setText("1");
         printBeautiState(f);
-        assertStateEquals("Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
-        assertOperatorsEqual("StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "strictClockUpDownOperator.c:noncoding", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "KappaScaler.s:1stpos", "gammaShapeScaler.s:1stpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:3rdpos", "gammaShapeScaler.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:1stpos", "FrequenciesExchanger.s:coding");
-        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:coding", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos", "FrequenciesPrior.s:coding", "FrequenciesPrior.s:1stpos", "FrequenciesPrior.s:2ndpos", "FrequenciesPrior.s:3rdpos");
-        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "clockRate.c:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
+        assertStateEquals("Tree.t:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
+        assertOperatorsEqual("YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "KappaScaler.s:1stpos", "gammaShapeScaler.s:1stpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:3rdpos", "gammaShapeScaler.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:1stpos", "FrequenciesExchanger.s:coding");
+        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleBirthRatePrior.t:3rdpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:coding", "YuleBirthRatePrior.t:1stpos", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos", "FrequenciesPrior.s:coding", "FrequenciesPrior.s:1stpos", "FrequenciesPrior.s:2ndpos", "FrequenciesPrior.s:3rdpos");
+        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
 
 
         // 4. clone second model to first model
@@ -87,15 +88,31 @@
         beautiFrame.button("ok").click();
         
         printBeautiState(f);
-        assertStateEquals("Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos");
-        assertOperatorsEqual("StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "strictClockUpDownOperator.c:noncoding", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "KappaScaler.s:1stpos", "gammaShapeScaler.s:1stpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:3rdpos", "gammaShapeScaler.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:1stpos");
-        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:coding", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos", "FrequenciesPrior.s:1stpos", "FrequenciesPrior.s:2ndpos", "FrequenciesPrior.s:3rdpos");
-        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "clockRate.c:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos");
+        assertStateEquals("Tree.t:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "birthRate.t:1stpos", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos");
+        assertOperatorsEqual("YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "KappaScaler.s:1stpos", "gammaShapeScaler.s:1stpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:3rdpos", "gammaShapeScaler.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:1stpos");
+        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleBirthRatePrior.t:3rdpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:coding", "YuleBirthRatePrior.t:1stpos", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos", "FrequenciesPrior.s:1stpos", "FrequenciesPrior.s:2ndpos", "FrequenciesPrior.s:3rdpos");
+        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos");
 
         makeSureXMLParses();       
 	}
 
 
+	/** robustly select rows -- don't give up after first attempt **/
+	private void selectRows(int ... rows) {
+		JTableFixture t = beautiFrame.table();
+		for (int attempt = 0; attempt < 5; attempt++) {
+			t.selectRows(rows);
+			if (t.target.getSelectedRowCount() == rows.length) {
+				return;
+			}
+			try {
+				Thread.sleep(500);
+			} catch (Exception e) {
+				
+			}
+		}
+	}
+
 	@Test
 	public void simpleClockModelCloneTest() throws Exception {
         warning("0. Load primate-mtDNA.nex");
@@ -108,16 +125,22 @@
 //	    	op.okButton().click();
 //	    }
 
+		// 0. link trees
+		f.selectTab("Partitions");
+		selectRows(0,1,2,3,4);
+		beautiFrame.button("Link Trees").click();
+
+		
         //1. Set the clock model of second partition to UCLD exponential
         warning("1. Set the clock model of second partition to UCLD exponential");
         f.selectTab("Clock Model");
         beautiFrame.list("listOfPartitions").selectItems(1);
         beautiFrame.comboBox().selectItem("Relaxed Clock Exponential");
         printBeautiState(f);
-        assertStateEquals("Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "ucedMean.c:noncoding", "expRateCategories.c:noncoding");
-        assertOperatorsEqual("StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "ucedMeanScaler.c:noncoding", "ExpCategoriesRandomWalk.c:noncoding", "ExpCategoriesSwapOperator.c:noncoding", "ExpCategoriesUniform.c:noncoding", "relaxedUpDownOperatorExp.c:noncoding");
-        assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "YuleBirthRatePrior.t:noncoding", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:coding", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "UCMeanRatePrior.c:noncoding");
-        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "ucedMean.c:noncoding", "rateStat.c:noncoding");
+        assertStateEquals("Tree.t:coding", "birthRate.t:coding", "clockRate.c:1stpos", "clockRate.c:3rdpos", "clockRate.c:2ndpos", "ucedMean.c:noncoding", "expRateCategories.c:noncoding");
+        assertOperatorsEqual("YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:1stpos", "strictClockUpDownOperator.c:1stpos", "StrictClockRateScaler.c:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:2ndpos", "strictClockUpDownOperator.c:2ndpos", "ucedMeanScaler.c:noncoding", "ExpCategoriesRandomWalk.c:noncoding", "ExpCategoriesSwapOperator.c:noncoding", "ExpCategoriesUniform.c:noncoding", "relaxedUpDownOperatorExp.c:noncoding");
+        assertPriorsEqual("YuleModel.t:coding", "YuleBirthRatePrior.t:coding", "ClockPrior.c:1stpos", "ClockPrior.c:3rdpos", "ClockPrior.c:2ndpos", "UCMeanRatePrior.c:noncoding");
+        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.1stpos", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.3rdpos", "treeLikelihood.2ndpos", "treeLikelihood.noncoding", "clockRate.c:1stpos", "clockRate.c:3rdpos", "clockRate.c:2ndpos", "ucedMean.c:noncoding", "rateStat.c:noncoding");
 
 
         //2. Clone to first and last partition 
@@ -125,21 +148,21 @@
         beautiFrame.comboBox().selectItem(1);
         beautiFrame.button("ok").click();
         printBeautiState(f);
-        assertStateEquals("birthRate.t:3rdpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "birthRate.t:coding", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "Tree.t:noncoding", "birthRate.t:noncoding", "ucedMean.c:noncoding", "expRateCategories.c:noncoding", "Tree.t:coding", "expRateCategories.c:coding", "ucedMean.c:3rdpos", "Tree.t:3rdpos", "expRateCategories.c:3rdpos");
-        assertOperatorsEqual("YuleBirthRateScaler.t:3rdpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "YuleBirthRateScaler.t:coding", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "ucedMeanScaler.c:noncoding", "ExpCategoriesRandomWalk.c:noncoding", "ExpCategoriesSwapOperator.c:noncoding", "ExpCategoriesUniform.c:noncoding", "relaxedUpDownOperatorExp.c:noncoding", "YuleModelTreeScaler.t:coding", "YuleModelNarrow.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelWilsonBalding.t:coding", "YuleModelSubtreeSlide.t:coding", "ExpCategoriesUniform.c:coding", "ExpCategoriesRandomWalk.c:coding", "ExpCategoriesSwapOperator.c:coding", "YuleModelWide.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelTreeScaler.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "ExpCategoriesUniform.c:3rdpos", "ExpCategoriesRandomWalk.c:3rdpos", "relaxedUpDownOperatorExp.c:3rdpos", "ExpCategoriesSwapOperator.c:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "ucedMeanScaler.c:3rdpos");
-        assertPriorsEqual("YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:coding", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:noncoding", "UCMeanRatePrior.c:noncoding", "YuleModel.t:coding", "YuleModel.t:3rdpos", "UCMeanRatePrior.c:3rdpos");
-        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "ucedMean.c:noncoding", "rateStat.c:noncoding", "rateStat.c:coding", "TreeHeight.t:coding", "YuleModel.t:coding", "rateStat.c:3rdpos", "ucedMean.c:3rdpos", "TreeHeight.t:3rdpos", "YuleModel.t:3rdpos");
-
+        assertStateEquals("Tree.t:coding", "birthRate.t:coding", "clockRate.c:2ndpos", "clockRate.c:1stpos", "ucedMean.c:noncoding", "expRateCategories.c:noncoding", "expRateCategories.c:coding", "ucedMean.c:3rdpos", "expRateCategories.c:3rdpos");
+        assertOperatorsEqual("YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:2ndpos", "strictClockUpDownOperator.c:2ndpos", "StrictClockRateScaler.c:1stpos", "strictClockUpDownOperator.c:1stpos", "ucedMeanScaler.c:noncoding", "ExpCategoriesRandomWalk.c:noncoding", "ExpCategoriesSwapOperator.c:noncoding", "ExpCategoriesUniform.c:noncoding", "relaxedUpDownOperatorExp.c:noncoding", "ExpCategoriesRandomWalk.c:coding", "ExpCategoriesSwapOperator.c:coding", "ExpCategoriesUniform.c:coding", "ucedMeanScaler.c:3rdpos", "ExpCategoriesRandomWalk.c:3rdpos", "ExpCategoriesSwapOperator.c:3rdpos", "ExpCategoriesUniform.c:3rdpos", "relaxedUpDownOperatorExp.c:3rdpos");
+        assertPriorsEqual("YuleModel.t:coding", "YuleBirthRatePrior.t:coding", "ClockPrior.c:2ndpos", "ClockPrior.c:1stpos", "UCMeanRatePrior.c:noncoding", "UCMeanRatePrior.c:3rdpos");
+        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.2ndpos", "treeLikelihood.noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "treeLikelihood.3rdpos", "clockRate.c:2ndpos", "clockRate.c:1stpos", "ucedMean.c:noncoding", "rateStat.c:noncoding", "rateStat.c:coding", "ucedMean.c:3rdpos", "rateStat.c:3rdpos");
+        
         
         //3. Set the clock model of third partition to UCLD lognormal
         warning("3. Set the clock model of third partition to UCLD lognormal");
         beautiFrame.list("listOfPartitions").selectItems(2);
         beautiFrame.comboBox().selectItem("Relaxed Clock Log Normal");
         printBeautiState(f);
-        assertStateEquals("Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "birthRate.t:coding", "Tree.t:1stpos", "birthRate.t:1stpos", "Tree.t:noncoding", "birthRate.t:noncoding", "birthRate.t:3rdpos", "ucedMean.c:noncoding", "expRateCategories.c:noncoding", "expRateCategories.c:coding", "Tree.t:coding", "expRateCategories.c:3rdpos", "Tree.t:3rdpos", "ucedMean.c:3rdpos", "ucldMean.c:1stpos", "ucldStdev.c:1stpos", "rateCategories.c:1stpos");
-        assertOperatorsEqual("StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "YuleBirthRateScaler.t:coding", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "YuleBirthRateScaler.t:3rdpos", "ucedMeanScaler.c:noncoding", "ExpCategoriesRandomWalk.c:noncoding", "ExpCategoriesSwapOperator.c:noncoding", "ExpCategoriesUniform.c:noncoding", "relaxedUpDownOperatorExp.c:noncoding", "YuleModelTreeRootScaler.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelTreeScaler.t:coding", "ExpCategoriesSwapOperator.c:coding", "ExpCategoriesRandomWalk.c:coding", "YuleModelUniformOperator.t:coding", "YuleModelWilsonBalding.t:coding", "YuleModelWide.t:coding", "YuleModelNarrow.t:coding", "ExpCategoriesUniform.c:coding", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "ExpCategoriesSwapOperator.c:3rdpos", "ExpCategoriesRandomWalk.c:3rdpos", "YuleModelUniformOperator.t:3rdpos", "ucedMeanScaler.c:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "relaxedUpDownOperatorExp.c:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "ExpCategoriesUniform.c:3rdpos", "ucldMeanScaler.c:1stpos", "ucldStdevScaler.c:1stpos", "CategoriesRandomWalk.c:1stpos", "CategoriesSwapOperator.c:1stpos", "CategoriesUniform.c:1stpos", "relaxedUpDownOperator.c:1stpos");
-        assertPriorsEqual("YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "YuleBirthRatePrior.t:coding", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:3rdpos", "UCMeanRatePrior.c:noncoding", "YuleModel.t:coding", "UCMeanRatePrior.c:3rdpos", "YuleModel.t:3rdpos", "ucldStdevPrior.c:1stpos", "MeanRatePrior.c:1stpos");
-        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.3rdpos", "birthRate.t:3rdpos", "ucedMean.c:noncoding", "rateStat.c:noncoding", "TreeHeight.t:coding", "rateStat.c:coding", "YuleModel.t:coding", "ucedMean.c:3rdpos", "TreeHeight.t:3rdpos", "rateStat.c:3rdpos", "YuleModel.t:3rdpos", "ucldMean.c:1stpos", "ucldStdev.c:1stpos", "rate.c:1stpos");
+        assertStateEquals("Tree.t:coding", "birthRate.t:coding", "clockRate.c:2ndpos", "ucedMean.c:noncoding", "expRateCategories.c:noncoding", "expRateCategories.c:coding", "ucedMean.c:3rdpos", "expRateCategories.c:3rdpos", "ucldMean.c:1stpos", "ucldStdev.c:1stpos", "rateCategories.c:1stpos");
+        assertOperatorsEqual("YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:2ndpos", "strictClockUpDownOperator.c:2ndpos", "ucedMeanScaler.c:noncoding", "ExpCategoriesRandomWalk.c:noncoding", "ExpCategoriesSwapOperator.c:noncoding", "ExpCategoriesUniform.c:noncoding", "relaxedUpDownOperatorExp.c:noncoding", "ExpCategoriesRandomWalk.c:coding", "ExpCategoriesSwapOperator.c:coding", "ExpCategoriesUniform.c:coding", "ucedMeanScaler.c:3rdpos", "ExpCategoriesRandomWalk.c:3rdpos", "ExpCategoriesSwapOperator.c:3rdpos", "ExpCategoriesUniform.c:3rdpos", "relaxedUpDownOperatorExp.c:3rdpos", "ucldMeanScaler.c:1stpos", "ucldStdevScaler.c:1stpos", "CategoriesRandomWalk.c:1stpos", "CategoriesSwapOperator.c:1stpos", "CategoriesUniform.c:1stpos", "relaxedUpDownOperator.c:1stpos");
+        assertPriorsEqual("YuleModel.t:coding", "YuleBirthRatePrior.t:coding", "ClockPrior.c:2ndpos", "UCMeanRatePrior.c:noncoding", "UCMeanRatePrior.c:3rdpos", "ucldStdevPrior.c:1stpos", "MeanRatePrior.c:1stpos");
+        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.2ndpos", "treeLikelihood.3rdpos", "treeLikelihood.noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "clockRate.c:2ndpos", "ucedMean.c:noncoding", "rateStat.c:noncoding", "rateStat.c:coding", "ucedMean.c:3rdpos", "rateStat.c:3rdpos", "ucldMean.c:1stpos", "ucldStdev.c:1stpos", "rate.c:1stpos");
 
         //4. Clone the third to fourth partition 
         warning("4. Clone the third to fourth partition");
@@ -147,6 +170,10 @@
         beautiFrame.comboBox().selectItem(2);
         beautiFrame.button("ok").click();
         printBeautiState(f);
+        assertStateEquals("Tree.t:coding", "birthRate.t:coding", "ucedMean.c:noncoding", "expRateCategories.c:noncoding", "expRateCategories.c:coding", "ucedMean.c:3rdpos", "expRateCategories.c:3rdpos", "ucldMean.c:1stpos", "ucldStdev.c:1stpos", "rateCategories.c:1stpos", "ucldMean.c:2ndpos", "ucldStdev.c:2ndpos", "rateCategories.c:2ndpos");
+        assertOperatorsEqual("YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "ucedMeanScaler.c:noncoding", "ExpCategoriesRandomWalk.c:noncoding", "ExpCategoriesSwapOperator.c:noncoding", "ExpCategoriesUniform.c:noncoding", "relaxedUpDownOperatorExp.c:noncoding", "ExpCategoriesRandomWalk.c:coding", "ExpCategoriesSwapOperator.c:coding", "ExpCategoriesUniform.c:coding", "ucedMeanScaler.c:3rdpos", "ExpCategoriesRandomWalk.c:3rdpos", "ExpCategoriesSwapOperator.c:3rdpos", "ExpCategoriesUniform.c:3rdpos", "relaxedUpDownOperatorExp.c:3rdpos", "ucldMeanScaler.c:1stpos", "ucldStdevScaler.c:1stpos", "CategoriesRandomWalk.c:1stpos", "CategoriesSwapOperator.c:1stpos", "CategoriesUniform.c:1stpos", "relaxedUpDownOperator.c:1stpos", "ucldMeanScaler.c:2ndpos", "ucldStdevScaler.c:2ndpos", "CategoriesRandomWalk.c:2ndpos", "CategoriesSwapOperator.c:2ndpos", "CategoriesUniform.c:2ndpos", "relaxedUpDownOperator.c:2ndpos");
+        assertPriorsEqual("YuleModel.t:coding", "YuleBirthRatePrior.t:coding", "UCMeanRatePrior.c:noncoding", "UCMeanRatePrior.c:3rdpos", "ucldStdevPrior.c:1stpos", "MeanRatePrior.c:1stpos", "ucldStdevPrior.c:2ndpos", "MeanRatePrior.c:2ndpos");
+        assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.2ndpos", "treeLikelihood.noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "treeLikelihood.3rdpos", "ucedMean.c:noncoding", "rateStat.c:noncoding", "rateStat.c:coding", "ucedMean.c:3rdpos", "rateStat.c:3rdpos", "ucldMean.c:1stpos", "ucldStdev.c:1stpos", "rate.c:1stpos", "ucldMean.c:2ndpos", "ucldStdev.c:2ndpos", "rate.c:2ndpos");
         
         
         makeSureXMLParses();
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/app/beauti/LinkUnlinkTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/app/beauti/LinkUnlinkTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/app/beauti/LinkUnlinkTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/app/beauti/LinkUnlinkTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -63,10 +63,10 @@
 		f.selectTab("Partitions");
 		beautiFrame.button("Unlink Site Models").click();
 		printBeautiState(f);
-		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47");
-		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47");
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47");
-		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47");
+		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47",  "birthRate.t:47");
+		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "YuleBirthRatePrior.t:47");
+		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "YuleModel.t:47", "birthRate.t:47");
 		
 		warning("Link clock models");
 		f.selectTab("Partitions");
@@ -77,10 +77,10 @@
 		f.selectTab("Partitions");
 		beautiFrame.button("Unlink Clock Models").click();
 		printBeautiState(f);
-		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47");
-		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47");
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47");
-		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47");
+		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47",  "birthRate.t:47");
+		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "YuleBirthRatePrior.t:47");
+		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "YuleModel.t:47", "birthRate.t:47");
 
 		warning("Link trees");
 		f.selectTab("Partitions");
@@ -91,10 +91,10 @@
 		f.selectTab("Partitions");
 		beautiFrame.button("Unlink Trees").click();
 		printBeautiState(f);
-		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47");
-		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47");
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47");
-		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47");
+		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47",  "birthRate.t:47");
+		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "YuleBirthRatePrior.t:47");
+		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "YuleModel.t:47", "birthRate.t:47");
 
 		makeSureXMLParses();
 	}
@@ -106,10 +106,10 @@
 
 		JTabbedPaneFixture f = beautiFrame.tabbedPane();
 		printBeautiState(f);
-		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47", "Tree.t:59", "clockRate.c:59", "birthRate.t:59");
-		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47", "StrictClockRateScaler.c:59", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59", "strictClockUpDownOperator.c:59");
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "ClockPrior.c:59", "YuleBirthRatePrior.t:59");
-		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "clockRate.c:59", "YuleModel.t:59", "birthRate.t:59");
+		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "birthRate.t:47", "Tree.t:59", "birthRate.t:59");
+		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "YuleBirthRatePrior.t:59");
+		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "YuleModel.t:59", "birthRate.t:59");
 
 		selectRows(0, 1, 2);
 
@@ -122,10 +122,10 @@
 		f.selectTab("Partitions");
 		beautiFrame.button("Unlink Site Models").click();
 		printBeautiState(f);
-		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47", "Tree.t:59", "clockRate.c:59", "birthRate.t:59");
-		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47", "StrictClockRateScaler.c:59", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59", "strictClockUpDownOperator.c:59");
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "ClockPrior.c:59", "YuleBirthRatePrior.t:59");
-		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "clockRate.c:59", "YuleModel.t:59", "birthRate.t:59");
+		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "birthRate.t:47", "Tree.t:59", "birthRate.t:59");
+		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "YuleBirthRatePrior.t:59");
+		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "YuleModel.t:59", "birthRate.t:59");
 		
 		warning("Link clock models");
 		f.selectTab("Partitions");
@@ -136,10 +136,10 @@
 		f.selectTab("Partitions");
 		beautiFrame.button("Unlink Clock Models").click();
 		printBeautiState(f);
-		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47", "Tree.t:59", "clockRate.c:59", "birthRate.t:59");
-		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47", "StrictClockRateScaler.c:59", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59", "strictClockUpDownOperator.c:59");
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "ClockPrior.c:59", "YuleBirthRatePrior.t:59");
-		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "clockRate.c:59", "YuleModel.t:59", "birthRate.t:59");
+		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "birthRate.t:47", "Tree.t:59", "birthRate.t:59");
+		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "YuleBirthRatePrior.t:59");
+		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "YuleModel.t:59", "birthRate.t:59");
 
 		warning("Link trees");
 		f.selectTab("Partitions");
@@ -150,10 +150,10 @@
 		f.selectTab("Partitions");
 		beautiFrame.button("Unlink Trees").click();
 		printBeautiState(f);
-		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47", "Tree.t:59", "clockRate.c:59", "birthRate.t:59");
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "ClockPrior.c:59", "YuleBirthRatePrior.t:59");
-		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47", "StrictClockRateScaler.c:59", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59", "strictClockUpDownOperator.c:59");
-		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "clockRate.c:59", "YuleModel.t:59", "birthRate.t:59");
+		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "birthRate.t:47", "Tree.t:59", "birthRate.t:59");
+		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "YuleBirthRatePrior.t:59");
+		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "YuleModel.t:59", "birthRate.t:59");
 
 		makeSureXMLParses();
 	}
@@ -217,10 +217,10 @@
 
 		JTabbedPaneFixture f = beautiFrame.tabbedPane();
 		printBeautiState(f);
-		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47", "Tree.t:59", "clockRate.c:59", "birthRate.t:59");
-		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47", "StrictClockRateScaler.c:59", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59", "strictClockUpDownOperator.c:59");
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "ClockPrior.c:59", "YuleBirthRatePrior.t:59");
-		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "clockRate.c:59", "YuleModel.t:59", "birthRate.t:59");
+		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "birthRate.t:47", "Tree.t:59", "birthRate.t:59");
+		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "YuleBirthRatePrior.t:59");
+		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "YuleModel.t:59", "birthRate.t:59");
 
 		selectRows(2, 1, 0);
 
@@ -257,10 +257,10 @@
 
 		JTabbedPaneFixture f = beautiFrame.tabbedPane();
 		printBeautiState(f);
-		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47", "Tree.t:59", "clockRate.c:59", "birthRate.t:59");
-		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47", "StrictClockRateScaler.c:59", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59", "strictClockUpDownOperator.c:59");
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "ClockPrior.c:59", "YuleBirthRatePrior.t:59");
-		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "clockRate.c:59", "YuleModel.t:59", "birthRate.t:59");
+		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "birthRate.t:47", "Tree.t:59", "birthRate.t:59");
+		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "YuleBirthRatePrior.t:59");
+		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47",  "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "YuleModel.t:59", "birthRate.t:59");
 
 		selectRows(0, 1, 2);
 
@@ -300,12 +300,12 @@
 
 		JTabbedPaneFixture f = beautiFrame.tabbedPane();
 		printBeautiState(f);
-		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47", "Tree.t:59", "clockRate.c:59", "birthRate.t:59");
-		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47", "StrictClockRateScaler.c:59", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59", "strictClockUpDownOperator.c:59");
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "ClockPrior.c:59", "YuleBirthRatePrior.t:59");
-		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "clockRate.c:59", "YuleModel.t:59", "birthRate.t:59");
+		assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "birthRate.t:47", "Tree.t:59", "birthRate.t:59");
+		assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "YuleBirthRateScaler.t:59", "YuleModelTreeScaler.t:59", "YuleModelTreeRootScaler.t:59", "YuleModelUniformOperator.t:59", "YuleModelSubtreeSlide.t:59", "YuleModelNarrow.t:59", "YuleModelWide.t:59", "YuleModelWilsonBalding.t:59");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "YuleBirthRatePrior.t:47", "YuleModel.t:59", "YuleBirthRatePrior.t:59");
+		assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "YuleModel.t:47", "birthRate.t:47", "treeLikelihood.59", "TreeHeight.t:59", "YuleModel.t:59", "birthRate.t:59");
 
-		assertParameterCountInPriorIs(5);		
+		assertParameterCountInPriorIs(3);		
 
 		selectRows(0, 1, 2);
 
@@ -451,7 +451,7 @@
 		selectRows(1);
 		beautiFrame.button("-").click();
 		printBeautiState(f);
-		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:59", "ClockPrior.c:59", "YuleBirthRatePrior.t:59");
+		assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:59", "YuleBirthRatePrior.t:59");
 
 		JTableFixture t = beautiFrame.table();
 		Assertions.assertThat(t.target.getRowCount()).isEqualTo(2);
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/ClockModelTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/ClockModelTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/ClockModelTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/ClockModelTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -1,11 +1,11 @@
 package test.beast.beast2vs1;
 
 
+import test.beast.beast2vs1.trace.Expectation;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import test.beast.beast2vs1.trace.Expectation;
-
 /**
  * @author Walter Xie
  */
@@ -48,10 +48,10 @@
                 addExpIntoList(expList, "tree.height", 6.32E-02, 6.76E-05);
                 addExpIntoList(expList, "popSize", 9.67E-02, 5.99E-04);
                 addExpIntoList(expList, "hky.kappa", 25.807, 0.1812);
-                addExpIntoList(expList, "hky.frequencies1", 0.327, 6.15E-04);
-                addExpIntoList(expList, "hky.frequencies2", 0.258, 6.09E-04);
-                addExpIntoList(expList, "hky.frequencies3", 0.155, 3.88E-04);
-                addExpIntoList(expList, "hky.frequencies4", 0.261, 5.17E-04);
+                addExpIntoList(expList, "hky.frequencies.1", 0.327, 6.15E-04);
+                addExpIntoList(expList, "hky.frequencies.2", 0.258, 6.09E-04);
+                addExpIntoList(expList, "hky.frequencies.3", 0.155, 3.88E-04);
+                addExpIntoList(expList, "hky.frequencies.4", 0.261, 5.17E-04);
                 addExpIntoList(expList, "clockRate", 1.0, 0.0);
                 addExpIntoList(expList, "treeLikelihood", -1816.691, 0.0522);
                 addExpIntoList(expList, "coalescent", 7.24, 9.58E-03);
@@ -75,10 +75,10 @@
                 addExpIntoList(expList, "tree.height", 6.4088E-2, 1.4663E-4);
                 addExpIntoList(expList, "popSize", 9.6541E-2, 6.6609E-4);
                 addExpIntoList(expList, "hky.kappa", 26.544, 0.2648);
-                addExpIntoList(expList, "hky.frequencies1", 0.3253, 7.3002E-4);
-                addExpIntoList(expList, "hky.frequencies2", 0.258, 5.5405E-4);
-                addExpIntoList(expList, "hky.frequencies3", 0.1546, 4.6881E-4);
-                addExpIntoList(expList, "hky.frequencies4", 0.262, 6.1501E-4);
+                addExpIntoList(expList, "hky.frequencies.1", 0.3253, 7.3002E-4);
+                addExpIntoList(expList, "hky.frequencies.2", 0.258, 5.5405E-4);
+                addExpIntoList(expList, "hky.frequencies.3", 0.1546, 4.6881E-4);
+                addExpIntoList(expList, "hky.frequencies.4", 0.262, 6.1501E-4);
                 addExpIntoList(expList, "treeLikelihood", -1816.5603, 5.5936E-2);
                 addExpIntoList(expList, "coalescent", 7.2815, 1.3472E-2);
                 break;
@@ -90,10 +90,10 @@
                 addExpIntoList(expList, "tree.height", 6.4535E-2, 4.3471E-4);
                 addExpIntoList(expList, "popSize", 9.4535E-2, 1.7803E-3);
                 addExpIntoList(expList, "hky.kappa", 26.0574, 0.2775);
-                addExpIntoList(expList, "hky.frequencies1", 0.3262, 9.4363E-4);
-                addExpIntoList(expList, "hky.frequencies2", 0.2575, 7.5592E-4);
-                addExpIntoList(expList, "hky.frequencies3", 0.1545, 5.1935E-4);
-                addExpIntoList(expList, "hky.frequencies4", 0.2618, 5.9827E-4);
+                addExpIntoList(expList, "hky.frequencies.1", 0.3262, 9.4363E-4);
+                addExpIntoList(expList, "hky.frequencies.2", 0.2575, 7.5592E-4);
+                addExpIntoList(expList, "hky.frequencies.3", 0.1545, 5.1935E-4);
+                addExpIntoList(expList, "hky.frequencies.4", 0.2618, 5.9827E-4);
                 addExpIntoList(expList, "S", 0.1786, 4.9947E-3);
                 addExpIntoList(expList, "coalescent", 7.3012, 3.0267E-2);
                 addExpIntoList(expList, "rate.mean", 0.9962, 3.1704E-3);
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/StarBEASTTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/StarBEASTTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/StarBEASTTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/StarBEASTTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -1,11 +1,11 @@
 package test.beast.beast2vs1;
 
 
+import test.beast.beast2vs1.trace.Expectation;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import test.beast.beast2vs1.trace.Expectation;
-
 /**
  * Due to different naming, *BEAST 2 speciesCoalescent != *BEAST 1 species.coalescent
  * <p/>
@@ -45,6 +45,7 @@
         super.setUp(XML_FILES);
     }
 
+    // Note: some parameter names are hard-coded in XML, so no dot, e.g. "hky.kappa26"
     @Override
 	protected List<Expectation> giveExpectations(int index_XML) throws Exception {
         List<Expectation> expList = new ArrayList<Expectation>();
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/SubstitutionModelTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/SubstitutionModelTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/SubstitutionModelTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/SubstitutionModelTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -1,11 +1,11 @@
 package test.beast.beast2vs1;
 
 
+import test.beast.beast2vs1.trace.Expectation;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import test.beast.beast2vs1.trace.Expectation;
-
 /**
  * @author Walter Xie
  */
@@ -67,15 +67,15 @@
                 addExpIntoList(expList, "prior", -8.24, 1.1349E-2);
                 addExpIntoList(expList, "TreeHeight.firsthalf", 0.2523, 1.2987E-4);
                 addExpIntoList(expList, "kappa.firsthalf", 4.8401, 1.184E-2);
-                addExpIntoList(expList, "freqParameter.firsthalf1", 0.289, 6.1115E-4);
-                addExpIntoList(expList, "freqParameter.firsthalf2", 0.3204, 6.8116E-4);
-                addExpIntoList(expList, "freqParameter.firsthalf3", 0.1081, 3.8843E-4);
-                addExpIntoList(expList, "freqParameter.firsthalf4", 0.2825, 5.1796E-4);
+                addExpIntoList(expList, "freqParameter.firsthalf.1", 0.289, 6.1115E-4);
+                addExpIntoList(expList, "freqParameter.firsthalf.2", 0.3204, 6.8116E-4);
+                addExpIntoList(expList, "freqParameter.firsthalf.3", 0.1081, 3.8843E-4);
+                addExpIntoList(expList, "freqParameter.firsthalf.4", 0.2825, 5.1796E-4);
                 addExpIntoList(expList, "kappa.secondhalf", 5.22, 1.121E-2);
-                addExpIntoList(expList, "freqParameter.secondhalf1", 0.3368, 6.3272E-4);
-                addExpIntoList(expList, "freqParameter.secondhalf2", 0.2646, 4.8458E-4);
-                addExpIntoList(expList, "freqParameter.secondhalf3", 0.1018, 2.8896E-4);
-                addExpIntoList(expList, "freqParameter.secondhalf4", 0.2968, 5.2109E-4);
+                addExpIntoList(expList, "freqParameter.secondhalf.1", 0.3368, 6.3272E-4);
+                addExpIntoList(expList, "freqParameter.secondhalf.2", 0.2646, 4.8458E-4);
+                addExpIntoList(expList, "freqParameter.secondhalf.3", 0.1018, 2.8896E-4);
+                addExpIntoList(expList, "freqParameter.secondhalf.4", 0.2968, 5.2109E-4);
                 addExpIntoList(expList, "likelihood", -5993.68, 8.1194E-2);
                 addExpIntoList(expList, "treeLikelihood.firsthalf", -3049.7192, 6.5715E-2);
                 addExpIntoList(expList, "treeLikelihood.secondhalf", -2943.9608, 5.2473E-2);
@@ -88,15 +88,15 @@
                 addExpIntoList(expList, "prior", 0.8416, 0.2033);
                 addExpIntoList(expList, "tree.height", 9.8986E-2, 3.709E-4);
                 addExpIntoList(expList, "CP12.hky.kappa", 25.0699, 0.2541);
-                addExpIntoList(expList, "CP12.frequencies1", 0.3444, 8.2165E-4);
-                addExpIntoList(expList, "CP12.frequencies2", 0.2447, 6.885E-4);
-                addExpIntoList(expList, "CP12.frequencies3", 0.1444, 5.3526E-4);
-                addExpIntoList(expList, "CP12.frequencies4", 0.2666, 6.174E-4);
+                addExpIntoList(expList, "CP12.frequencies.1", 0.3444, 8.2165E-4);
+                addExpIntoList(expList, "CP12.frequencies.2", 0.2447, 6.885E-4);
+                addExpIntoList(expList, "CP12.frequencies.3", 0.1444, 5.3526E-4);
+                addExpIntoList(expList, "CP12.frequencies.4", 0.2666, 6.174E-4);
                 addExpIntoList(expList, "CP3.hky.kappa", 82.9907, 1.9773);
-                addExpIntoList(expList, "CP3.frequencies1", 0.3197, 1.1763E-3);
-                addExpIntoList(expList, "CP3.frequencies2", 0.264, 9.0478E-4);
-                addExpIntoList(expList, "CP3.frequencies3", 0.1675, 8.6506E-4);
-                addExpIntoList(expList, "CP3.frequencies4", 0.2488, 1.059E-3);
+                addExpIntoList(expList, "CP3.frequencies.1", 0.3197, 1.1763E-3);
+                addExpIntoList(expList, "CP3.frequencies.2", 0.264, 9.0478E-4);
+                addExpIntoList(expList, "CP3.frequencies.3", 0.1675, 8.6506E-4);
+                addExpIntoList(expList, "CP3.frequencies.4", 0.2488, 1.059E-3);
                 addExpIntoList(expList, "CP12.gammaShape", 6.4322E-2, 4.8796E-3);
                 addExpIntoList(expList, "CP3.gammaShape", 8.5652E-2, 6.9946E-3);
                 addExpIntoList(expList, "CP12.mutationRate", 0.9437, 1.195E-3);
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/TaxonOrderTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/TaxonOrderTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/TaxonOrderTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/TaxonOrderTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -1,11 +1,11 @@
 package test.beast.beast2vs1;
 
 
+import test.beast.beast2vs1.trace.Expectation;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import test.beast.beast2vs1.trace.Expectation;
-
 public class TaxonOrderTest extends TestFramework {
 
     private final String[] XML_FILES = new String[]{"testStarBeast2.xml"};
@@ -20,6 +20,7 @@
         super.setUp(XML_FILES);
     }
 
+    // Note: some parameter names are hard-coded in XML, so no dot, e.g. "hky.kappa26"
     @Override
 	protected List<Expectation> giveExpectations(int index_XML) throws Exception {
         List<Expectation> expList = new ArrayList<Expectation>();
@@ -40,21 +41,21 @@
                 addExpIntoList(expList, "hky.kappa26",4.4936,0.0744);
                 addExpIntoList(expList, "hky.kappa29",4.0749,0.0588);
                 /*
-                addExpIntoList(expList, "popSize1",0.0040487,0.00027109);
-                addExpIntoList(expList, "popSize2",0.0062535,0.00026144);
-                addExpIntoList(expList, "popSize3",0.0023299,0.00015953);
-                addExpIntoList(expList, "popSize4",0.0029275,0.00023455);
-                addExpIntoList(expList, "popSize5",0.0021888,0.00022018);
-                addExpIntoList(expList, "popSize6",0.0042746,0.00018535);
-                addExpIntoList(expList, "popSize7",0.004097,0.00035926);
-                addExpIntoList(expList, "popSize8",0.0041803,0.00022475);
-                addExpIntoList(expList, "popSize9",0.0036424,0.00016521);
-                addExpIntoList(expList, "popSize10",0.0037575,0.00032465);
-                addExpIntoList(expList, "popSize11",0.0035904,0.00017545);
-                addExpIntoList(expList, "popSize12",0.0036104,0.00020949);
-                addExpIntoList(expList, "popSize13",0.0040485,0.00019889);
-                addExpIntoList(expList, "popSize14",0.0035229,0.00017978);
-                addExpIntoList(expList, "popSize15",0.005072,0.00017682);
+                addExpIntoList(expList, "popSize.1",0.0040487,0.00027109);
+                addExpIntoList(expList, "popSize.2",0.0062535,0.00026144);
+                addExpIntoList(expList, "popSize.3",0.0023299,0.00015953);
+                addExpIntoList(expList, "popSize.4",0.0029275,0.00023455);
+                addExpIntoList(expList, "popSize.5",0.0021888,0.00022018);
+                addExpIntoList(expList, "popSize.6",0.0042746,0.00018535);
+                addExpIntoList(expList, "popSize.7",0.004097,0.00035926);
+                addExpIntoList(expList, "popSize.8",0.0041803,0.00022475);
+                addExpIntoList(expList, "popSize.9",0.0036424,0.00016521);
+                addExpIntoList(expList, "popSize.10",0.0037575,0.00032465);
+                addExpIntoList(expList, "popSize.11",0.0035904,0.00017545);
+                addExpIntoList(expList, "popSize.12",0.0036104,0.00020949);
+                addExpIntoList(expList, "popSize.13",0.0040485,0.00019889);
+                addExpIntoList(expList, "popSize.14",0.0035229,0.00017978);
+                addExpIntoList(expList, "popSize.15",0.005072,0.00017682);
                 */
                 addExpIntoList(expList, "TreeHeightSP",0.0118,0.00025562);
                 addExpIntoList(expList, "TreeHeight26",0.0266,0.00010397);
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/TestFramework.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/TestFramework.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/TestFramework.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/TestFramework.java	2022-04-04 07:18:36.000000000 +0000
@@ -1,8 +1,5 @@
 package test.beast.beast2vs1;
 
-import java.io.File;
-import java.util.List;
-
 import beagle.BeagleFlag;
 import beast.core.Logger;
 import beast.util.Randomizer;
@@ -11,9 +8,13 @@
 import junit.framework.TestCase;
 import test.beast.beast2vs1.trace.Expectation;
 import test.beast.beast2vs1.trace.LogAnalyser;
+import test.beast.beast2vs1.trace.TraceStatistics;
+
+import java.io.File;
+import java.util.List;
 
 public abstract class TestFramework extends TestCase {
-    protected static long SEED = 128;
+    protected long SEED = 128;
     private String[] xmls;
 
     protected abstract List<Expectation> giveExpectations(int index_XML) throws Exception;
@@ -29,24 +30,26 @@
     	logDir = System.getProperty("user.dir");
     }
     
-    protected void setUp(String[] xmls) { // throws Exception {
+    protected void setUp(String[] xmls) throws InterruptedException { // throws Exception {
         this.xmls = new String[xmls.length];
         for (int i = 0; i < xmls.length; i++) {
             this.xmls[i] = xmls[i];
         }
+        Thread.sleep(1000); // ensure log file is processed between test suits
     }
 //    protected abstract void analyse() throws Exception;
 
     public void analyse(int index_XML) throws Exception {
 //        for (int i = 0; i < xmls.length; i++) {
 //            if (giveExpectations(i).size() > 0) {
+        // quick fix to ensure log file names are different
+        SEED = SEED + index_XML;
         Randomizer.setSeed(SEED);
         Logger.FILE_MODE = Logger.LogFileMode.overwrite;
         
         long beagleFlags = BeagleFlag.PROCESSOR_CPU.getMask() | BeagleFlag.VECTOR_SSE.getMask();
         System.setProperty("beagle.preferred.flags", Long.toString(beagleFlags));
 
-
         String fileName = dirName + xmls[index_XML];
 
         System.out.println("Processing " + fileName);
@@ -62,14 +65,22 @@
         LogAnalyser logAnalyser = new LogAnalyser(logFile, giveExpectations(index_XML)); // burnIn = 0.1 * maxState
 
         for (Expectation expectation : logAnalyser.m_pExpectations.get()) {
-            Assert.assertTrue(xmls[index_XML] + ": Expected " + expectation.traceName.get() + " delta mean: "
-                    + expectation.expValue.get() + " - " + expectation.getTraceStatistics().getMean()
-                    + " <= delta stdErr: 2*(" + expectation.getStdError() + " + "
-                    + expectation.getTraceStatistics().getStdErrorOfMean() + ")", expectation.isPassed());
-
-            if (checkESS)
-            	Assert.assertTrue(xmls[index_XML] + ":  has very low effective sample sizes (ESS) "
-                    + expectation.getTraceStatistics().getESS(), expectation.isValid());
+            TraceStatistics stats = expectation.getTraceStatistics();
+            if (stats == null) {
+                System.err.println("Null trace at " + expectation.traceName.get()
+                        + "\nPlease check log for " + xmls[index_XML] );
+            } else {
+                double m = stats.getMean();
+                double stderr = stats.getStdErrorOfMean();
+
+                Assert.assertTrue(xmls[index_XML] + ": Expected " + expectation.traceName.get() + " delta mean: "
+                        + expectation.expValue.get() + " - " + m + " <= delta stdErr: 2*(" + expectation.getStdError()
+                        + " + " + stderr + ")", expectation.isPassed());
+
+                if (checkESS)
+                    Assert.assertTrue(xmls[index_XML] + ":  has very low effective sample sizes (ESS) "
+                            + stats.getESS(), expectation.isValid());
+            }
         }
 
         System.out.println("\nSucceed " + fileName);
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/TipTimeTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/TipTimeTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/TipTimeTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/TipTimeTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -1,11 +1,11 @@
 package test.beast.beast2vs1;
 
 
+import test.beast.beast2vs1.trace.Expectation;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import test.beast.beast2vs1.trace.Expectation;
-
 /**
  * @author Walter Xie
  */
@@ -64,10 +64,10 @@
                 addExpIntoList(expList, "tree.height", 68.2541, 8.7152E-2);
                 addExpIntoList(expList, "popSize", 33.9172, 0.1266);
                 addExpIntoList(expList, "hky.kappa", 17.2562, 7.7984E-2);
-                addExpIntoList(expList, "hky.frequencies1", 0.2838, 4.3904E-4);
-                addExpIntoList(expList, "hky.frequencies2", 0.2116, 3.8223E-4);
-                addExpIntoList(expList, "hky.frequencies3", 0.2516, 4.0877E-4);
-                addExpIntoList(expList, "hky.frequencies4", 0.253, 4.1631E-4);
+                addExpIntoList(expList, "hky.frequencies.1", 0.2838, 4.3904E-4);
+                addExpIntoList(expList, "hky.frequencies.2", 0.2116, 3.8223E-4);
+                addExpIntoList(expList, "hky.frequencies.3", 0.2516, 4.0877E-4);
+                addExpIntoList(expList, "hky.frequencies.4", 0.253, 4.1631E-4);
                 addExpIntoList(expList, "clockRate", 8.1277E-4, 1.405E-6);
                 addExpIntoList(expList, "treeLikelihood", -3850.8083, 6.0429E-2);
                 addExpIntoList(expList, "coalescent", -71.6925, 3.5705E-2);
@@ -88,10 +88,10 @@
                 addExpIntoList(expList, "tree.height", 10.848, 5.6709E-2);
                 addExpIntoList(expList, "popSize", 9.4786, 0.1178);
                 addExpIntoList(expList, "hky.kappa", 8.906, 4.4495E-2);
-                addExpIntoList(expList, "hky.frequencies1", 0.3433, 4.5468E-4);
-                addExpIntoList(expList, "hky.frequencies2", 0.1857, 3.3512E-4);
-                addExpIntoList(expList, "hky.frequencies3", 0.2229, 4.1666E-4);
-                addExpIntoList(expList, "hky.frequencies4", 0.2481, 4.3418E-4);
+                addExpIntoList(expList, "hky.frequencies.1", 0.3433, 4.5468E-4);
+                addExpIntoList(expList, "hky.frequencies.2", 0.1857, 3.3512E-4);
+                addExpIntoList(expList, "hky.frequencies.3", 0.2229, 4.1666E-4);
+                addExpIntoList(expList, "hky.frequencies.4", 0.2481, 4.3418E-4);
                 addExpIntoList(expList, "clockRate", 3.6834E-3, 2.8931E-5);
 //                addExpIntoList(expList, "height(TREESPARROW_HENAN_1_2004)", 2005 - 1.502, 2.8594E-2);
                 addExpIntoList(expList, "height(CHICKEN_HONGKONG_915_1997)", 2005 - 8.1493, 1.0676E-2);
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/TreePriorTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/TreePriorTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/TreePriorTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/TreePriorTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -1,11 +1,11 @@
 package test.beast.beast2vs1;
 
 
+import test.beast.beast2vs1.trace.Expectation;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import test.beast.beast2vs1.trace.Expectation;
-
 /**
  * @author Walter Xie
  */
@@ -68,10 +68,10 @@
                 addExpIntoList(expList, "tree.height", 0.06318, 6.73E-05);
                 addExpIntoList(expList, "popSize", 0.0979, 6.38E-04);
                 addExpIntoList(expList, "hky.kappa", 26.262, 0.2217);
-                addExpIntoList(expList, "hky.frequencies1", 0.326, 6.04E-04);
-                addExpIntoList(expList, "hky.frequencies2", 0.258, 5.23E-04);
-                addExpIntoList(expList, "hky.frequencies3", 0.155, 4.03E-04);
-                addExpIntoList(expList, "hky.frequencies4", 0.261, 5.64E-04);
+                addExpIntoList(expList, "hky.frequencies.1", 0.326, 6.04E-04);
+                addExpIntoList(expList, "hky.frequencies.2", 0.258, 5.23E-04);
+                addExpIntoList(expList, "hky.frequencies.3", 0.155, 4.03E-04);
+                addExpIntoList(expList, "hky.frequencies.4", 0.261, 5.64E-04);
                 addExpIntoList(expList, "treeLikelihood", -1816.764, 0.0556);
                 addExpIntoList(expList, "coalescent", 7.242, 9.94E-03);
                 break;
@@ -82,10 +82,10 @@
                 addExpIntoList(expList, "tree.height", 6.35E-02, 6.61E-05);
                 addExpIntoList(expList, "popSize", 0.132, 0.2987);
                 addExpIntoList(expList, "hky.kappa", 33.139, 0.1812);
-                addExpIntoList(expList, "hky.frequencies1", 0.326, 5.70E-04);
-                addExpIntoList(expList, "hky.frequencies2", 0.257, 6.15E-04);
-                addExpIntoList(expList, "hky.frequencies3", 0.154, 4.17E-04);
-                addExpIntoList(expList, "hky.frequencies4", 0.262, 4.91E-04);
+                addExpIntoList(expList, "hky.frequencies.1", 0.326, 5.70E-04);
+                addExpIntoList(expList, "hky.frequencies.2", 0.257, 6.15E-04);
+                addExpIntoList(expList, "hky.frequencies.3", 0.154, 4.17E-04);
+                addExpIntoList(expList, "hky.frequencies.4", 0.262, 4.91E-04);
                 addExpIntoList(expList, "treeLikelihood", -1816.698, 5.82E-02);
                 addExpIntoList(expList, "coalescent", 6.948, 1.24E-02);
                 break;
@@ -98,10 +98,10 @@
                 addExpIntoList(expList, "popSize", 1.0231, 5.1484E-2);
                 addExpIntoList(expList, "growthRate", 58.5276, 0.6012);
                 addExpIntoList(expList, "hky.kappa", 26.301, 0.211);
-                addExpIntoList(expList, "hky.frequencies1", 0.3266, 5.9862E-4);
-                addExpIntoList(expList, "hky.frequencies2", 0.2569, 5.3533E-4);
-                addExpIntoList(expList, "hky.frequencies3", 0.154, 4.0839E-4);
-                addExpIntoList(expList, "hky.frequencies4", 0.2625, 5.7627E-4);
+                addExpIntoList(expList, "hky.frequencies.1", 0.3266, 5.9862E-4);
+                addExpIntoList(expList, "hky.frequencies.2", 0.2569, 5.3533E-4);
+                addExpIntoList(expList, "hky.frequencies.3", 0.154, 4.0839E-4);
+                addExpIntoList(expList, "hky.frequencies.4", 0.2625, 5.7627E-4);
                 addExpIntoList(expList, "treeLikelihood", -1816.7188, 4.9732E-2);
                 addExpIntoList(expList, "coalescent", 9.4203, 1.31E-2);
                 break;
@@ -131,16 +131,16 @@
                 addExpIntoList(expList, "prior", -92.178, 7.5174E-2);
                 addExpIntoList(expList, "siteModel.alpha", 5.4354E-2, 5.2519E-4);
                 addExpIntoList(expList, "clock.rate", 9.4858E-4, 1.9706E-6);
-                addExpIntoList(expList, "skyline.popSize1", 67.8827, 2.2639);
-                addExpIntoList(expList, "skyline.popSize2", 25.4281, 0.3165);
-                addExpIntoList(expList, "skyline.popSize3", 31.9271, 0.3819);
-                addExpIntoList(expList, "skyline.popSize4", 41.6596, 0.3976);
-                addExpIntoList(expList, "skyline.popSize5", 33.5967, 0.3554);
-                addExpIntoList(expList, "skyline.groupSize1", 2.4686, 4.0465E-2); 
-                addExpIntoList(expList, "skyline.groupSize2", 3.3671, 3.9454E-2); 
-                addExpIntoList(expList, "skyline.groupSize3", 3.181, 3.3807E-2); // TODO diff bigger than 2*delta
-                addExpIntoList(expList, "skyline.groupSize4", 3.723, 5.0187E-2);
-                addExpIntoList(expList, "skyline.groupSize5", 3.2603, 5.9824E-2);
+                addExpIntoList(expList, "skyline.popSize.1", 67.8827, 2.2639);
+                addExpIntoList(expList, "skyline.popSize.2", 25.4281, 0.3165);
+                addExpIntoList(expList, "skyline.popSize.3", 31.9271, 0.3819);
+                addExpIntoList(expList, "skyline.popSize.4", 41.6596, 0.3976);
+                addExpIntoList(expList, "skyline.popSize.5", 33.5967, 0.3554);
+                addExpIntoList(expList, "skyline.groupSize.1", 2.4686, 4.0465E-2);
+                addExpIntoList(expList, "skyline.groupSize.2", 3.3671, 3.9454E-2);
+                addExpIntoList(expList, "skyline.groupSize.3", 3.181, 3.3807E-2); // TODO diff bigger than 2*delta
+                addExpIntoList(expList, "skyline.groupSize.4", 3.723, 5.0187E-2);
+                addExpIntoList(expList, "skyline.groupSize.5", 3.2603, 5.9824E-2);
                 addExpIntoList(expList, "hky.kappa", 21.6911, 5.2142E-2);
                 addExpIntoList(expList, "treeModel.rootHeight", 70.3393, 0.1057);
                 addExpIntoList(expList, "likelihood", -3773.1854, 3.9474E-2);
@@ -153,41 +153,46 @@
                 addExpIntoList(expList, "posterior", -1809.8121, 7.6417E-2);
                 addExpIntoList(expList, "prior", 7.0426, 3.7042E-2);
                 addExpIntoList(expList, "tree.height", 6.2187E-2, 6.4148E-5);
-                addExpIntoList(expList, "popSizes1", 0.2084, 4.4215E-3);
-                addExpIntoList(expList, "popSizes2", 0.1012, 1.1132E-3);
-                addExpIntoList(expList, "popSizes3", 5.0552E-2, 7.8572E-4);
-                addExpIntoList(expList, "groupSizes1", 1.7396, 8.2581E-3);
+                addExpIntoList(expList, "popSizes.1", 0.2084, 4.4215E-3);
+                addExpIntoList(expList, "popSizes.2", 0.1012, 1.1132E-3);
+                addExpIntoList(expList, "popSizes.3", 5.0552E-2, 7.8572E-4);
+                addExpIntoList(expList, "groupSizes.1", 1.7396, 8.2581E-3);
                 //addExpIntoList(expList, "groupSizes2", 1.78, 8.3052E-3); // TODO diff bigger than 2*delta
-                addExpIntoList(expList, "groupSizes3", 1.4804, 7.7151E-3);
+                addExpIntoList(expList, "groupSizes.3", 1.4804, 7.7151E-3);
                 addExpIntoList(expList, "hky.kappa", 26.0187, 0.2286);
-                addExpIntoList(expList, "hky.frequencies1", 0.3262, 7.0596E-4);
-                addExpIntoList(expList, "hky.frequencies2", 0.2571, 5.876E-4);
-                addExpIntoList(expList, "hky.frequencies3", 0.1546, 4.8206E-4);
-                addExpIntoList(expList, "hky.frequencies4", 0.262, 5.9621E-4);
+                addExpIntoList(expList, "hky.frequencies.1", 0.3262, 7.0596E-4);
+                addExpIntoList(expList, "hky.frequencies.2", 0.2571, 5.876E-4);
+                addExpIntoList(expList, "hky.frequencies.3", 0.1546, 4.8206E-4);
+                addExpIntoList(expList, "hky.frequencies.4", 0.262, 5.9621E-4);
                 addExpIntoList(expList, "treeLikelihood", -1816.8547, 6.3527E-2);
                 addExpIntoList(expList, "skyline", 7.9513, 1.6384E-2);
                 addExpIntoList(expList, "eml1", 5.059, 2.1669E-2);
                 break;
 
             case 8: // testEBSP.xml
-//        BEAST 1 testEBSP.xml
-                addExpIntoList(expList, "posterior", -1826.2014, 0.1562);
-                addExpIntoList(expList, "prior", -9.4517, 0.1782);
-                addExpIntoList(expList, "tree.height", 6.3528E-2, 7.0709E-5);
-                addExpIntoList(expList, "popSizes1", 2435.0409, 132.4556);
-                addExpIntoList(expList, "popSizes2", 2195.7116, 156.2106);
-                addExpIntoList(expList, "popSizes3", 1065.3511, 119.8768);
-                addExpIntoList(expList, "indicators", 1.3275, 2.1211E-2);
-                addExpIntoList(expList, "indicators", 1.5219, 2.9634E-2);
-                addExpIntoList(expList, "indicators", 2.1505, 3.8185E-2);
-                addExpIntoList(expList, "hky.kappa", 26.4814, 0.2725);
-                addExpIntoList(expList, "hky.frequencies1", 0.3252, 7.7972E-4);
-                addExpIntoList(expList, "hky.frequencies2", 0.2581, 5.685E-4);
-                addExpIntoList(expList, "hky.frequencies3", 0.1553, 4.3071E-4);
-                addExpIntoList(expList, "hky.frequencies4", 0.2614, 6.1733E-4);
-                addExpIntoList(expList, "treeLikelihood", -1816.7497, 5.4764E-2);
-                // this is clearly bunk (negative value for a positive parameter)
-                addExpIntoList(expList, "populationMean", -3.4472, 0.1802);
+                // all values below are from BEAST 1.8.4, testEBSP.xml
+                addExpIntoList(expList, "posterior", -3831.4728, 9.7013);
+                addExpIntoList(expList, "prior", 458.7546, 9.6924);
+                addExpIntoList(expList, "tree.26.height", 0.0275, 7.7632E-5);
+                addExpIntoList(expList, "tree.29.height", 0.0231, 6.589E-5);
+                addExpIntoList(expList, "tree.47.height", 0.0263, 6.5618E-5);
+                addExpIntoList(expList, "sum(indicators)", 0.4738, 0.0187);
+                addExpIntoList(expList, "populationMean", 0.0443, 0.0119);
+                addExpIntoList(expList, "treeLikelihood.26", -1264.9419, 0.0819);
+                addExpIntoList(expList, "treeLikelihood.29", -1246.7234, 0.0754);
+                addExpIntoList(expList, "treeLikelihood.47", -1778.562, 0.0951);
+                addExpIntoList(expList, "coalescent", 220.5613, 0.1462);
+                addExpIntoList(expList, "popSizes.1", 0.0172, 3.9108E-3);
+                addExpIntoList(expList, "popSizes.2", 0.0444, 0.0136);
+                addExpIntoList(expList, "popSizes.3", 0.0397, 0.0103);
+                addExpIntoList(expList, "indicators.1", 6.3871E-3, 1.7047E-3);
+                addExpIntoList(expList, "indicators.2", 0.0192, 9.1203E-3);
+                addExpIntoList(expList, "indicators.3", 9.4418E-3, 2.2312E-3);
+                addExpIntoList(expList, "hky.kappa.26", 4.4946, 0.038);
+                addExpIntoList(expList, "hky.frequencies.26.1", 0.4099, 8.0594E-4);
+                addExpIntoList(expList, "hky.frequencies.26.2", 0.2064, 6.2073E-4);
+                addExpIntoList(expList, "hky.frequencies.26.3", 0.1754, 5.6823E-4);
+                addExpIntoList(expList, "hky.frequencies.26.4", 0.2083, 6.139E-4);
                 break;
 
 
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/TreeTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/TreeTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/TreeTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/TreeTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -1,11 +1,11 @@
 package test.beast.beast2vs1;
 
 
+import test.beast.beast2vs1.trace.Expectation;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import test.beast.beast2vs1.trace.Expectation;
-
 /**
  * @author Walter Xie
  */
@@ -40,10 +40,10 @@
                 addExpIntoList(expList, "mrcatime(human,chimp)", 2.0326E-2, 3.5906E-5);
                 addExpIntoList(expList, "popSize", 9.7862E-2, 6.2387E-4);
                 addExpIntoList(expList, "hky.kappa", 25.8288, 0.1962);
-                addExpIntoList(expList, "hky.frequencies1", 0.3262, 5.9501E-4);
-                addExpIntoList(expList, "hky.frequencies2", 0.2569, 5.0647E-4);
-                addExpIntoList(expList, "hky.frequencies3", 0.1552, 4.4638E-4);
-                addExpIntoList(expList, "hky.frequencies4", 0.2617, 5.1085E-4);
+                addExpIntoList(expList, "hky.frequencies.1", 0.3262, 5.9501E-4);
+                addExpIntoList(expList, "hky.frequencies.2", 0.2569, 5.0647E-4);
+                addExpIntoList(expList, "hky.frequencies.3", 0.1552, 4.4638E-4);
+                addExpIntoList(expList, "hky.frequencies.4", 0.2617, 5.1085E-4);
                 addExpIntoList(expList, "likelihood", -1816.6943, 5.8444E-2);
                 addExpIntoList(expList, "coalescent", 7.2378, 9.1912E-3);
                 break;
@@ -56,10 +56,10 @@
                 addExpIntoList(expList, "mrcatime(human,chimp)", 1.7069E-2, 3.3455E-5);
                 addExpIntoList(expList, "popSize", 0.1049, 6.4588E-4);
                 addExpIntoList(expList, "hky.kappa", 26.7792, 0.1851);
-                addExpIntoList(expList, "hky.frequencies1", 0.328, 7.1121E-4);
-                addExpIntoList(expList, "hky.frequencies2", 0.2573, 5.4356E-4);
-                addExpIntoList(expList, "hky.frequencies3", 0.1548, 4.2604E-4);
-                addExpIntoList(expList, "hky.frequencies4", 0.2599, 6.0174E-4);
+                addExpIntoList(expList, "hky.frequencies.1", 0.328, 7.1121E-4);
+                addExpIntoList(expList, "hky.frequencies.2", 0.2573, 5.4356E-4);
+                addExpIntoList(expList, "hky.frequencies.3", 0.1548, 4.2604E-4);
+                addExpIntoList(expList, "hky.frequencies.4", 0.2599, 6.0174E-4);
                 addExpIntoList(expList, "likelihood", -1828.7667, 6.527E-2);
                 addExpIntoList(expList, "coalescent", 6.864, 9.7699E-3);
                 break;
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/tutorials/DivergenceDatingTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/tutorials/DivergenceDatingTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/tutorials/DivergenceDatingTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/tutorials/DivergenceDatingTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -13,7 +13,7 @@
     @Test
     public void DivergenceDatingTutorial() throws Exception {
         DivergenceDatingRunner runner = new DivergenceDatingRunner(org.fest.util.Files.temporaryFolder());
-        runner.analyse(0);
+        runner.analyse(0); // SEED = SEED + index_XML;
     }
 
     // This is for debugging the test only
@@ -28,7 +28,7 @@
 
     class DivergenceDatingRunner extends TestFramework {
 
-        DivergenceDatingRunner(File file) {
+        DivergenceDatingRunner(File file) throws InterruptedException {
             super();
             setUp(new String[]{"/x.xml"});
             dirName = file.getPath();
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/tutorials/RateTutorialTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/tutorials/RateTutorialTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/tutorials/RateTutorialTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/tutorials/RateTutorialTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -29,7 +29,7 @@
 
     class MEPRunner extends TestFramework {
 
-        MEPRunner(File file) {
+        MEPRunner(File file) throws InterruptedException {
             super();
             setUp(new String[]{"/x.xml"});
             dirName = file.getPath();
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/tutorials/StarBeastTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/tutorials/StarBeastTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/beast2vs1/tutorials/StarBeastTest.java	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/beast2vs1/tutorials/StarBeastTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -28,7 +28,7 @@
 
     class StarBEASTRunner extends TestFramework {
 
-        StarBEASTRunner(File file) {
+        StarBEASTRunner(File file) throws InterruptedException {
             super();
             setUp(new String[]{"/x.xml"});
             dirName = file.getPath();
diff -Nru beast2-mcmc-2.6.6+dfsg/src/test/beast/core/DirectSimulatorTest.java beast2-mcmc-2.6.7+dfsg/src/test/beast/core/DirectSimulatorTest.java
--- beast2-mcmc-2.6.6+dfsg/src/test/beast/core/DirectSimulatorTest.java	1970-01-01 00:00:00.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/src/test/beast/core/DirectSimulatorTest.java	2022-04-04 07:18:36.000000000 +0000
@@ -0,0 +1,90 @@
+package test.beast.core;
+
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+
+import beast.core.DirectSimulator;
+import beast.core.Logger;
+import beast.core.Logger.LogFileMode;
+import beast.core.parameter.RealParameter;
+import beast.math.distributions.Normal;
+import beast.math.distributions.Prior;
+import beast.util.LogAnalyser;
+import junit.framework.TestCase;
+
+public class DirectSimulatorTest extends TestCase {
+
+	@Rule
+	public TemporaryFolder folder = new TemporaryFolder();
+
+	
+	@Test
+	public void testBoundedPrior() throws Exception {
+		RealParameter p = new RealParameter("0.0");
+		p.setID("p");
+		p.setUpper(0.0);
+		p.setLower(Double.NEGATIVE_INFINITY);
+		
+		Normal normal = new Normal();
+		normal.initByName("mean", "0.0", "sigma", "1.0");
+		Prior prior = new Prior();
+		prior.initByName("x", p, "distr", normal);
+		
+		Logger logger = new Logger();
+		Logger.FILE_MODE = LogFileMode.overwrite;
+		String tracefile = "/tmp/trace.log";
+		logger.initByName("log", p, "fileName", tracefile);
+				
+		
+		DirectSimulator simulator = new DirectSimulator();
+		simulator.initByName("distribution", prior, "logger", logger, "nSamples", 1000);
+		
+		simulator.run();
+
+		LogAnalyser trace = new LogAnalyser(tracefile);
+		double upper = trace.get95HPDup("p");
+		assertEquals(true, upper <= 0);
+		
+		// clean up
+		// new File(tracefile).delete();
+		System.err.println("done");
+		
+	}
+
+	@Test
+	public void testMultiDimensionalBoundedPrior() throws Exception {
+		RealParameter x = new RealParameter();
+		x.initByName("dimension", 3, "value", "0.0", "upper", 0.0, "lower", Double.NEGATIVE_INFINITY);
+		x.setID("x");
+		
+		Normal normal = new Normal();
+		normal.initByName("mean", "0.0", "sigma", "1.0");
+		Prior prior = new Prior();
+		prior.initByName("x", x, "distr", normal);
+		
+		Logger logger = new Logger();
+		Logger.FILE_MODE = LogFileMode.overwrite;
+		String tracefile = "/tmp/trace.log";
+		logger.initByName("log", x, "fileName", tracefile);
+				
+		
+		DirectSimulator simulator = new DirectSimulator();
+		simulator.initByName("distribution", prior, "logger", logger, "nSamples", 1000);
+		
+		simulator.run();
+
+		LogAnalyser trace = new LogAnalyser(tracefile);
+		double upper = trace.get95HPDup("x.1");
+		assertEquals(true, upper <= 0);
+		upper = trace.get95HPDup("x.2");
+		assertEquals(true, upper <= 0);
+		upper = trace.get95HPDup("x.3");
+		assertEquals(true, upper <= 0);
+		
+		// clean up
+		// new File(tracefile).delete();
+		System.err.println("done");
+		
+	}
+}
diff -Nru beast2-mcmc-2.6.6+dfsg/version.xml beast2-mcmc-2.6.7+dfsg/version.xml
--- beast2-mcmc-2.6.6+dfsg/version.xml	2021-08-11 20:11:54.000000000 +0000
+++ beast2-mcmc-2.6.7+dfsg/version.xml	2022-04-04 07:18:36.000000000 +0000
@@ -1 +1 @@
-<addon name='BEAST' version='2.6.6' url="https://github.com/CompEvol/beast2/releases/download/v2.6.6/BEAST.v2.6.6.package.zip"/>
+<addon name='BEAST' version='2.6.7' url="https://github.com/CompEvol/beast2/releases/download/v2.6.7/BEAST.v2.6.7.package.zip"/>