diff -Nru bppsuite-2.4.1/debian/changelog bppsuite-2.4.1/debian/changelog
--- bppsuite-2.4.1/debian/changelog	2020-09-15 13:26:51.000000000 +0000
+++ bppsuite-2.4.1/debian/changelog	2022-02-16 07:50:02.000000000 +0000
@@ -1,3 +1,14 @@
+bppsuite (2.4.1-4) unstable; urgency=medium
+
+  * Fix watchfile to detect new versions on github
+  * Exclude tag v3.0.0 to be considered a new version
+    (see https://github.com/BioPP/bppsuite/issues/14#issuecomment-1041137412)
+  * Standards-Version: 4.6.0 (routine-update)
+  * Build-Depends: libeigen3-dev
+  * Enable uscan to create a sensible download name
+
+ -- Andreas Tille <tille@debian.org>  Wed, 16 Feb 2022 08:50:02 +0100
+
 bppsuite (2.4.1-3) unstable; urgency=medium
 
   * Approximate autopkgtest output. Closes: #963088.
diff -Nru bppsuite-2.4.1/debian/control bppsuite-2.4.1/debian/control
--- bppsuite-2.4.1/debian/control	2020-09-15 13:26:51.000000000 +0000
+++ bppsuite-2.4.1/debian/control	2022-02-16 07:50:02.000000000 +0000
@@ -8,9 +8,10 @@
 Build-Depends: debhelper-compat (= 13),
                cmake,
                texinfo,
-               libbpp-phyl-dev (>= 2.4.0),
-               libbpp-popgen-dev (>= 2.4.0)
-Standards-Version: 4.5.0
+               libbpp-phyl-dev,
+               libbpp-popgen-dev,
+               libeigen3-dev
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/bppsuite
 Vcs-Git: https://salsa.debian.org/med-team/bppsuite.git
 Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
diff -Nru bppsuite-2.4.1/debian/patches/fix_includes_path.patch bppsuite-2.4.1/debian/patches/fix_includes_path.patch
--- bppsuite-2.4.1/debian/patches/fix_includes_path.patch	1970-01-01 00:00:00.000000000 +0000
+++ bppsuite-2.4.1/debian/patches/fix_includes_path.patch	2022-02-16 07:50:02.000000000 +0000
@@ -0,0 +1,98 @@
+--- a/bppSuite/bppConsense.cpp
++++ b/bppSuite/bppConsense.cpp
+@@ -53,8 +53,8 @@ using namespace std;
+ #include <Bpp/Text/KeyvalTools.h>
+ 
+ // From PhylLib:
+-#include <Bpp/Phyl/Tree/Tree.h>
+-#include <Bpp/Phyl/Tree/TreeTemplate.h>
++#include <Bpp/Phyl/Tree.h>
++#include <Bpp/Phyl/TreeTemplate.h>
+ #include <Bpp/Phyl/Io/Newick.h>
+ #include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>
+ 
+--- a/bppSuite/bppDist.cpp
++++ b/bppSuite/bppDist.cpp
+@@ -64,7 +64,7 @@ using namespace std;
+ 
+ 
+ // From PhylLib:
+-#include <Bpp/Phyl/Tree/Tree.h>
++#include <Bpp/Phyl/Tree.h>
+ #include <Bpp/Phyl/PatternTools.h>
+ #include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>
+ #include <Bpp/Phyl/Io/Newick.h>
+--- a/bppSuite/bppMixedLikelihoods.cpp
++++ b/bppSuite/bppMixedLikelihoods.cpp
+@@ -68,8 +68,8 @@ using namespace std;
+ 
+ // From bpp-phyl:
+ #include <Bpp/Phyl/App/BppPhylogeneticsApplication.h>
+-#include <Bpp/Phyl/Tree/Tree.h>
+-#include <Bpp/Phyl/Tree/TreeTemplate.h>
++#include <Bpp/Phyl/Tree.h>
++#include <Bpp/Phyl/TreeTemplate.h>
+ #include <Bpp/Phyl/PatternTools.h>
+ #include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>
+ #include <Bpp/Phyl/OptimizationTools.h>
+--- a/bppSuite/bppPars.cpp
++++ b/bppSuite/bppPars.cpp
+@@ -60,7 +60,7 @@ using namespace std;
+ #include <Bpp/Seq/App/SequenceApplicationTools.h>
+ 
+ // From PhylLib:
+-#include <Bpp/Phyl/Tree/Tree.h>
++#include <Bpp/Phyl/Tree.h>
+ #include <Bpp/Phyl/PatternTools.h>
+ #include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>
+ #include <Bpp/Phyl/OptimizationTools.h>
+--- a/bppSuite/bppPopStats.cpp
++++ b/bppSuite/bppPopStats.cpp
+@@ -61,7 +61,7 @@ using namespace std;
+ #include <Bpp/Seq/App/SequenceApplicationTools.h>
+ 
+ // From bpp-phyl:
+-#include <Bpp/Phyl/Tree/Tree.h>
++#include <Bpp/Phyl/Tree.h>
+ #include <Bpp/Phyl/Model/Nucleotide/K80.h>
+ #include <Bpp/Phyl/Model/Codon/YN98.h>
+ #include <Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h>
+--- a/bppSuite/bppReRoot.cpp
++++ b/bppSuite/bppReRoot.cpp
+@@ -53,10 +53,10 @@ using namespace std;
+ #include <Bpp/App/ApplicationTools.h>
+ 
+ // From PhylLib:
+-#include <Bpp/Phyl/Tree/Tree.h>
+-#include <Bpp/Phyl/Tree/Node.h>
+-#include <Bpp/Phyl/Tree/TreeExceptions.h>
+-#include <Bpp/Phyl/Tree/TreeTemplateTools.h>
++#include <Bpp/Phyl/Tree.h>
++#include <Bpp/Phyl/Node.h>
++#include <Bpp/Phyl/TreeExceptions.h>
++#include <Bpp/Phyl/TreeTemplateTools.h>
+ // From bpp-phyl:
+ #include <Bpp/Phyl/Io/Newick.h>
+ #include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>
+--- a/bppSuite/bppSeqMan.cpp
++++ b/bppSuite/bppSeqMan.cpp
+@@ -63,7 +63,7 @@ using namespace std;
+ #include <Bpp/Seq/SequenceTools.h>
+ 
+ //From bpp-phyl:
+-#include <Bpp/Phyl/Tree/Tree.h>
++#include <Bpp/Phyl/Tree.h>
+ #include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>
+ 
+ using namespace bpp;
+--- a/bppSuite/bppTreeDraw.cpp
++++ b/bppSuite/bppTreeDraw.cpp
+@@ -52,7 +52,7 @@ using namespace std;
+ #include <Bpp/Graphics/Fig/XFigGraphicDevice.h>
+ 
+ // From bpp-phyl:
+-#include <Bpp/Phyl/Tree/Tree.h>
++#include <Bpp/Phyl/Tree.h>
+ 
+ #include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>
+ #include <Bpp/Phyl/Graphics/PhylogramPlot.h>
diff -Nru bppsuite-2.4.1/debian/patches/series bppsuite-2.4.1/debian/patches/series
--- bppsuite-2.4.1/debian/patches/series	2018-04-10 12:50:41.000000000 +0000
+++ bppsuite-2.4.1/debian/patches/series	2022-02-16 07:50:02.000000000 +0000
@@ -0,0 +1 @@
+# fix_includes_path.patch
diff -Nru bppsuite-2.4.1/debian/watch bppsuite-2.4.1/debian/watch
--- bppsuite-2.4.1/debian/watch	2017-06-14 12:25:57.000000000 +0000
+++ bppsuite-2.4.1/debian/watch	2022-02-16 07:50:02.000000000 +0000
@@ -1,3 +1,4 @@
 version=4
 
-https://github.com/BioPP/bppsuite/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+opts="uversionmangle=s/3.0.0/0.3.0.0/,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \
+  https://github.com/BioPP/bppsuite/releases .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)