--- embassy-phylip-3.69+20100721.orig/debian/copyright +++ embassy-phylip-3.69+20100721/debian/copyright @@ -0,0 +1,48 @@ +Format: http://dep.debian.net/deps/dep5/ +Source: ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.tar.gz +Disclaimer : This package is not part of the Debian operating system. + . + The embassy-phylip source and binary Debian packages are part of the + “non-free” area in the Debian archive. The packages in this area are not part + of the Debian system, although they have been configured for use with Debian. + We nevertheless support the use of the seaview source and binary Debian + packages and provide infrastructure for non-free packages (such as our bug + tracking system and mailing lists). The licence of PHYLIPNEW does not forbid + Debian from using autobuilders to create binary packages. +Comment: It was confirmed on the EMBOSS User mailing list that the COPYING file + (GNU GPL) is there by error and the Phylip copyright file applies on all the + package. http://lists.open-bio.org/pipermail/emboss/2009-August/003713.html + +Files: * +Copyright: © 1993-2004 by the University of Washington. +License: Phylip + Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. + Permission is granted to copy and use this program provided no fee is + charged for it and provided that this copyright notice is not removed. + +Files: doc/*, emboss-doc/* +Copyright: 1986-2002 by the University of Washington. +License: Phylip-doc + Written by Joseph Felsenstein. Permission is granted to copy this document + provided that no fee is charged for it and that this copyright notice is not + removed. + +Files: debian/* +Copyright: 2009–2011 Charles Plessy +License: BOLA-1.0 + This work is provided 'as-is', without any express or implied warranty. In no + event will the authors be held liable for any damages arising from the use of + this work. + . + To all effects and purposes, this work is to be considered Public Domain. + . + . + However, if you want to be "buena onda", you should: + . + 1. Not take credit for it, and give proper recognition to the authors. + 2. Share your modifications, so everybody benefits from them. + 3. Do something nice for the authors. + 4. Help someone who needs it. + 5. Don't waste. Anything, but specially energy that comes from natural + non-renewable resources. + 6. Be tolerant. Everything that's good in nature comes from cooperation. --- embassy-phylip-3.69+20100721.orig/debian/embassy-phylip.manpages +++ embassy-phylip-3.69+20100721/debian/embassy-phylip.manpages @@ -0,0 +1,40 @@ +debian/manpages/fclique.1e +debian/manpages/fconsense.1e +debian/manpages/fcontml.1e +debian/manpages/fcontrast.1e +debian/manpages/fdiscboot.1e +debian/manpages/fdnacomp.1e +debian/manpages/fdnadist.1e +debian/manpages/fdnainvar.1e +debian/manpages/fdnaml.1e +debian/manpages/fdnamlk.1e +debian/manpages/fdnamove.1e +debian/manpages/fdnapars.1e +debian/manpages/fdnapenny.1e +debian/manpages/fdollop.1e +debian/manpages/fdolmove.1e +debian/manpages/fdolpenny.1e +debian/manpages/fdrawgram.1e +debian/manpages/fdrawtree.1e +debian/manpages/ffactor.1e +debian/manpages/ffitch.1e +debian/manpages/ffreqboot.1e +debian/manpages/fgendist.1e +debian/manpages/fkitsch.1e +debian/manpages/fmix.1e +debian/manpages/fmove.1e +debian/manpages/fneighbor.1e +debian/manpages/fpars.1e +debian/manpages/fpenny.1e +debian/manpages/fproml.1e +debian/manpages/fpromlk.1e +debian/manpages/fprotdist.1e +debian/manpages/fprotpars.1e +debian/manpages/frestboot.1e +debian/manpages/frestdist.1e +debian/manpages/frestml.1e +debian/manpages/fretree.1e +debian/manpages/fseqboot.1e +debian/manpages/fseqbootall.1e +debian/manpages/ftreedist.1e +debian/manpages/ftreedistpair.1e --- embassy-phylip-3.69+20100721.orig/debian/changelog +++ embassy-phylip-3.69+20100721/debian/changelog @@ -0,0 +1,55 @@ +embassy-phylip (3.69+20100721-3build1) precise; urgency=low + + * Rebuild for libmysqlclient transition + + -- Clint Byrum Wed, 23 Nov 2011 23:28:47 -0800 + +embassy-phylip (3.69+20100721-3) unstable; urgency=low + + * Set RPATH with “-Wl,--rpath” as GCC 4.6 does not accept “-R” anymore. + (debian/rules) LP: #770835. + * Incremented Standards-Version to reflect conformance with Policy 3.9.2 + (debian/control, no changes needed). + * Updated debian/embassy-phylip.lintian-overrides for lintian 2.5. + * debian/copyright validated with config-edit. + + -- Charles Plessy Thu, 12 May 2011 14:19:59 +0900 + +embassy-phylip (3.69+20100721-2) unstable; urgency=low + + * Built on emboss-lib 6.3.1-6, pre-emptively depending on versions + lower than 6.3.2, because backwards compatibility is sometimes + broken (debian/control, debian/rules). + * Set an RPATH to /usr/lib/emboss/lib for using EMBOSS private + libraries (debian/rules, debian/embassy-phylip.lintian-overrides). + * Refreshed debian/copyright to test the latest DEP-5 format. + + -- Charles Plessy Thu, 23 Sep 2010 14:07:26 +0900 + +embassy-phylip (3.69+20100721-1) unstable; urgency=low + + * New upstream release in which the version number was unchanged. + * Build-Depends on emboss 6.3.1 (debian/control, debian/rules). + * Build-Depends on libmysqlclient-dev and libpq-dev until emboss is fixed. + * Pass -Wl,--as-needed to avoid unneeded binary dependencies (debian/rules). + * Incremented Standards-Version to reflect conformance with Policy 3.9.1 + (debian/control, no changes needed). + + -- Charles Plessy Wed, 11 Aug 2010 19:46:37 +0900 + +embassy-phylip (3.69-1) unstable; urgency=low + + * New upstream release. + * debian/control: + - Corrected Vcs-Browser URL. + - Incremented Standards-Version to reflect conformance with Policy 3.8.4 + (no changes needed). + * Refreshed the manual pages (Debian-specific). + + -- Charles Plessy Tue, 01 Jun 2010 21:43:33 +0900 + +embassy-phylip (3.68-1) unstable; urgency=low + + * Initial release (Closes: #493977) + + -- Charles Plessy Sat, 08 Aug 2009 16:59:11 +0900 --- embassy-phylip-3.69+20100721.orig/debian/control +++ embassy-phylip-3.69+20100721/debian/control @@ -0,0 +1,40 @@ +Source: embassy-phylip +Section: non-free/science +Priority: optional +Maintainer: Debian Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Charles Plessy +Build-Depends: + cdbs, + debhelper (>= 7), + autotools-dev, + libxaw7-dev, + emboss-lib (>= 6.3.1-6~), + emboss-lib (<< 6.3.2~), + libgd2-xpm-dev, + libmysqlclient-dev, + libpq-dev +Standards-Version: 3.9.2 +Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#PHYLIPNEW +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-phylip/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-phylip/trunk + +Package: embassy-phylip +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib (>= 6.3.1-6~), emboss-lib (<< 6.3.2~) +Description: EMBOSS conversions of the programs in the phylip package + This package is the adaptation of the PHYLIP package in which its + programs can operate with the biological sequence formats and databases + of the European Molecular Biology Open Software Suite (EMBOSS). The + software packages adapted for EMBOSS are called EMBASSY. + . + PHYLIP (the PHYLogeny Inference Package) is a package of programs for + inferring phylogenies (evolutionary trees). Methods that are available + in the package include parsimony, distance matrix, and likelihood + methods, including bootstrapping and consensus trees. Data types that + can be handled include molecular sequences, gene frequencies, + restriction sites and fragments, distance matrices, and discrete + characters. + . + The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them + from the original programs and avoid namespace conflict. --- embassy-phylip-3.69+20100721.orig/debian/rules +++ embassy-phylip-3.69+20100721/debian/rules @@ -0,0 +1,9 @@ +#!/usr/bin/make -f + +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/class/autotools.mk + +DEB_CONFIGURE_EXTRA_FLAGS = --enable-systemlibs + +CFLAGS += -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot -L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib +LDFLAGS += -Wl,--as-needed --- embassy-phylip-3.69+20100721.orig/debian/embassy-phylip.lintian-overrides +++ embassy-phylip-3.69+20100721/debian/embassy-phylip.lintian-overrides @@ -0,0 +1,3 @@ +# The embassy packages use privately some of the EMBOSS libraries. They have +# the same upstream authors and are released together. +embassy-phylip: binary-or-shlib-defines-rpath * --- embassy-phylip-3.69+20100721.orig/debian/compat +++ embassy-phylip-3.69+20100721/debian/compat @@ -0,0 +1 @@ +7 --- embassy-phylip-3.69+20100721.orig/debian/watch +++ embassy-phylip-3.69+20100721/debian/watch @@ -0,0 +1,2 @@ +version=3 +ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-(.*).tar.gz --- embassy-phylip-3.69+20100721.orig/debian/docs +++ embassy-phylip-3.69+20100721/debian/docs @@ -0,0 +1,2 @@ +ChangeLog +README --- embassy-phylip-3.69+20100721.orig/debian/manpages/frestml.1e +++ embassy-phylip-3.69+20100721/debian/manpages/frestml.1e @@ -0,0 +1,143 @@ +'\" t +.\" Title: FRESTML +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FRESTML" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +frestml \- Restriction site maximum Likelihood method +.SH "SYNOPSIS" +.HP \w'\fBfrestml\fR\ 'u +\fBfrestml\fR \fB\-data\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-njumble\ \fR\fB\fIinteger\fR\fR] \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-allsites\ \fR\fB\fIboolean\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-sitelength\ \fR\fB\fIinteger\fR\fR] \fB\-global\ \fR\fB\fIboolean\fR\fR \fB\-rough\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfrestml\fR\ 'u +\fBfrestml\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfrestml\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-data\fR \fIdiscretestates\fR +.RS 4 +File containing one or more sets of restriction data +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-allsites\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-lengths\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-sitelength\fR \fIinteger\fR +.RS 4 +Default value: 6 +.RE +.PP +\fB\-global\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-rough\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +frestml is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fseqboot.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fseqboot.1e @@ -0,0 +1,140 @@ +'\" t +.\" Title: FSEQBOOT +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FSEQBOOT" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fseqboot \- Bootstrapped sequences algorithm +.SH "SYNOPSIS" +.HP \w'\fBfseqboot\fR\ 'u +\fBfseqboot\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-categories\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-rewriteformat\ \fR\fB\fIlist\fR\fR \fB\-seqtype\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfseqboot\fR\ 'u +\fBfseqboot\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfseqboot\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqset\fR +.RS 4 +.RE +.PP +\fB\-categories\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file +.RE +.SS "Additional section" +.PP +\fB\-test\fR \fIlist\fR +.RS 4 +Default value: b +.RE +.PP +\fB\-regular\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-fracsample\fR \fIfloat\fR +.RS 4 +Default value: 100\&.0 +.RE +.PP +\fB\-rewriteformat\fR \fIlist\fR +.RS 4 +Default value: p +.RE +.PP +\fB\-seqtype\fR \fIlist\fR +.RS 4 +Default value: d +.RE +.PP +\fB\-blocksize\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-reps\fR \fIinteger\fR +.RS 4 +Default value: 100 +.RE +.PP +\fB\-justweights\fR \fIlist\fR +.RS 4 +Default value: d +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-dotdiff\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fseqboot is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/ffreqboot.1e +++ embassy-phylip-3.69+20100721/debian/manpages/ffreqboot.1e @@ -0,0 +1,126 @@ +'\" t +.\" Title: FFREQBOOT +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FFREQBOOT" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +ffreqboot \- Bootstrapped genetic frequencies algorithm +.SH "SYNOPSIS" +.HP \w'\fBffreqboot\fR\ 'u +\fBffreqboot\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBffreqboot\fR\ 'u +\fBffreqboot\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBffreqboot\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIfrequencies\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file +.RE +.SS "Additional section" +.PP +\fB\-test\fR \fIlist\fR +.RS 4 +Default value: b +.RE +.PP +\fB\-regular\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-fracsample\fR \fIfloat\fR +.RS 4 +Default value: 100\&.0 +.RE +.PP +\fB\-blocksize\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-reps\fR \fIinteger\fR +.RS 4 +Default value: 100 +.RE +.PP +\fB\-justweights\fR \fIlist\fR +.RS 4 +Default value: d +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-dotdiff\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +ffreqboot is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdnamlk.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdnamlk.1e @@ -0,0 +1,211 @@ +'\" t +.\" Title: FDNAMLK +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDNAMLK" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdnamlk \- Estimates nucleotide phylogeny by maximum likelihood +.SH "SYNOPSIS" +.HP \w'\fBfdnamlk\fR\ 'u +\fBfdnamlk\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ttratio\ \fR\fB\fIfloat\fR\fR] [\fB\-freqsfrom\ \fR\fB\fItoggle\fR\fR] \fB\-basefreq\ \fR\fB\fIarray\fR\fR [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR \fB\-lengths\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfdnamlk\fR\ 'u +\fBfdnamlk\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdnamlk\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-ncategories\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-rate\fR \fIarray\fR +.RS 4 +.RE +.PP +\fB\-categories\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-ttratio\fR \fIfloat\fR +.RS 4 +Default value: 2\&.0 +.RE +.PP +\fB\-freqsfrom\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-basefreq\fR \fIarray\fR +.RS 4 +Default value: 0\&.25 0\&.25 0\&.25 0\&.25 +.RE +.PP +\fB\-gamma\fR \fIlist\fR +.RS 4 +Default value: Constant rate +.RE +.PP +\fB\-gammacoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-ngammacat\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-invarcoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-ninvarcat\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-invarfrac\fR \fIfloat\fR +.RS 4 +Default value: 0\&.0 +.RE +.PP +\fB\-nhmmcategories\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-hmmrates\fR \fIarray\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-hmmprobabilities\fR \fIarray\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-adjsite\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-lambda\fR \fIfloat\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-global\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-lengths\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-hypstate\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdnamlk is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdnadist.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdnadist.1e @@ -0,0 +1,146 @@ +'\" t +.\" Title: FDNADIST +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDNADIST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdnadist \- Nucleic acid sequence Distance Matrix program +.SH "SYNOPSIS" +.HP \w'\fBfdnadist\fR\ 'u +\fBfdnadist\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-gamma\ \fR\fB\fIlist\fR\fR \fB\-ncategories\ \fR\fB\fIinteger\fR\fR \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-ttratio\ \fR\fB\fIfloat\fR\fR \fB\-freqsfrom\ \fR\fB\fItoggle\fR\fR \fB\-basefreq\ \fR\fB\fIarray\fR\fR [\fB\-lower\ \fR\fB\fIboolean\fR\fR] [\fB\-humanreadable\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfdnadist\fR\ 'u +\fBfdnadist\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdnadist\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: F84 distance model +.RE +.PP +\fB\-gamma\fR \fIlist\fR +.RS 4 +Default value: No distribution parameters used +.RE +.PP +\fB\-ncategories\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-rate\fR \fIarray\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-categories\fR \fIproperties\fR +.RS 4 +File of substitution rate categories +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-gammacoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-invarfrac\fR \fIfloat\fR +.RS 4 +Default value: 0\&.0 +.RE +.PP +\fB\-ttratio\fR \fIfloat\fR +.RS 4 +Default value: 2\&.0 +.RE +.PP +\fB\-freqsfrom\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-basefreq\fR \fIarray\fR +.RS 4 +Default value: 0\&.25 0\&.25 0\&.25 0\&.25 +.RE +.PP +\fB\-lower\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-humanreadable\fR \fIboolean\fR +.RS 4 +Default value: @($(method)==s?Y:N) +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdnadist is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdolpenny.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdolpenny.1e @@ -0,0 +1,144 @@ +'\" t +.\" Title: FDOLPENNY +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDOLPENNY" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdolpenny \- Penny algorithm Dollo or polymorphism +.SH "SYNOPSIS" +.HP \w'\fBfdolpenny\fR\ 'u +\fBfdolpenny\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-howmany\ \fR\fB\fIinteger\fR\fR] [\fB\-howoften\ \fR\fB\fIinteger\fR\fR] [\fB\-simple\ \fR\fB\fIboolean\fR\fR] [\fB\-method\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfdolpenny\fR\ 'u +\fBfdolpenny\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdolpenny\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIdiscretestates\fR +.RS 4 +File containing one or more data sets +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-ancfile\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-thresh\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-howmany\fR \fIinteger\fR +.RS 4 +Default value: 1000 +.RE +.PP +\fB\-howoften\fR \fIinteger\fR +.RS 4 +Default value: 100 +.RE +.PP +\fB\-simple\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: d +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-ancseq\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-stepbox\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdolpenny is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fpenny.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fpenny.1e @@ -0,0 +1,146 @@ +'\" t +.\" Title: FPENNY +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FPENNY" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fpenny \- Penny algorithm, branch\-and\-bound +.SH "SYNOPSIS" +.HP \w'\fBfpenny\fR\ 'u +\fBfpenny\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-howmany\ \fR\fB\fIinteger\fR\fR] [\fB\-howoften\ \fR\fB\fIinteger\fR\fR] [\fB\-simple\ \fR\fB\fIboolean\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfpenny\fR\ 'u +\fBfpenny\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfpenny\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIdiscretestates\fR +.RS 4 +File containing one or more data sets +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-ancfile\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-mixfile\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: Wagner +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-howmany\fR \fIinteger\fR +.RS 4 +Default value: 1000 +.RE +.PP +\fB\-howoften\fR \fIinteger\fR +.RS 4 +Default value: 100 +.RE +.PP +\fB\-simple\fR \fIboolean\fR +.RS 4 +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: $(infile\&.discretesize) +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-stepbox\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-ancseq\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fpenny is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdnacomp.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdnacomp.1e @@ -0,0 +1,127 @@ +'\" t +.\" Title: FDNACOMP +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDNACOMP" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdnacomp \- DNA compatibility algorithm +.SH "SYNOPSIS" +.HP \w'\fBfdnacomp\fR\ 'u +\fBfdnacomp\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-weights\ \fR\fB\fIproperties\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfdnacomp\fR\ 'u +\fBfdnacomp\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdnacomp\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-stepbox\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-ancseq\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdnacomp is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/ftreedist.1e +++ embassy-phylip-3.69+20100721/debian/manpages/ftreedist.1e @@ -0,0 +1,100 @@ +'\" t +.\" Title: FTREEDIST +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FTREEDIST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +ftreedist \- Distances between trees +.SH "SYNOPSIS" +.HP \w'\fBftreedist\fR\ 'u +\fBftreedist\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-dtype\ \fR\fB\fIlist\fR\fR] [\fB\-pairing\ \fR\fB\fIlist\fR\fR] [\fB\-style\ \fR\fB\fIlist\fR\fR] [\fB\-noroot\ \fR\fB\fIboolean\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBftreedist\fR\ 'u +\fBftreedist\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBftreedist\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Consensus" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-dtype\fR \fIlist\fR +.RS 4 +Default value: b +.RE +.PP +\fB\-pairing\fR \fIlist\fR +.RS 4 +Default value: a +.RE +.PP +\fB\-style\fR \fIlist\fR +.RS 4 +Default value: v +.RE +.PP +\fB\-noroot\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +ftreedist is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fpars.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fpars.1e @@ -0,0 +1,162 @@ +'\" t +.\" Title: FPARS +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FPARS" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fpars \- Discrete character parsimony +.SH "SYNOPSIS" +.HP \w'\fBfpars\fR\ 'u +\fBfpars\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR [\fB\-maxtrees\ \fR\fB\fIinteger\fR\fR] \fB\-thorough\ \fR\fB\fItoggle\fR\fR \fB\-rearrange\ \fR\fB\fIboolean\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR +.HP \w'\fBfpars\fR\ 'u +\fBfpars\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfpars\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIdiscretestates\fR +.RS 4 +File containing one or more data sets +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: Wagner +.RE +.PP +\fB\-maxtrees\fR \fIinteger\fR +.RS 4 +Default value: 100 +.RE +.PP +\fB\-thorough\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-rearrange\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-thresh\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-stepbox\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-ancseq\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-dotdiff\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fpars is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fcontrast.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fcontrast.1e @@ -0,0 +1,106 @@ +'\" t +.\" Title: FCONTRAST +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FCONTRAST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fcontrast \- Continuous character Contrasts +.SH "SYNOPSIS" +.HP \w'\fBfcontrast\fR\ 'u +\fBfcontrast\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-varywithin\ \fR\fB\fIboolean\fR\fR] \fB\-reg\ \fR\fB\fIboolean\fR\fR \fB\-writecont\ \fR\fB\fIboolean\fR\fR \fB\-nophylo\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfcontrast\fR\ 'u +\fBfcontrast\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfcontrast\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Continuous characters" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIfrequencies\fR +.RS 4 +File containing one or more sets of data +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-varywithin\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-reg\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-writecont\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-nophylo\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fcontrast is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fmix.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fmix.1e @@ -0,0 +1,145 @@ +'\" t +.\" Title: FMIX +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FMIX" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fmix \- Mixed parsimony algorithm +.SH "SYNOPSIS" +.HP \w'\fBfmix\fR\ 'u +\fBfmix\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfmix\fR\ 'u +\fBfmix\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfmix\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIdiscretestates\fR +.RS 4 +File containing one or more data sets +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-ancfile\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-mixfile\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: Wagner +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: $(infile\&.discretesize) +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-ancseq\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-stepbox\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fmix is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdrawtree.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdrawtree.1e @@ -0,0 +1,181 @@ +'\" t +.\" Title: FDRAWTREE +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDRAWTREE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdrawtree \- Plots an unrooted tree diagram +.SH "SYNOPSIS" +.HP \w'\fBfdrawtree\fR\ 'u +\fBfdrawtree\fR \fB\-fontfile\ \fR\fB\fIstring\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-plotfile\ \fR\fB\fIoutfile\fR\fR [\fB\-plotter\ \fR\fB\fIlist\fR\fR] [\fB\-previewer\ \fR\fB\fIlist\fR\fR] [\fB\-iterate\ \fR\fB\fIlist\fR\fR] [\fB\-lengths\ \fR\fB\fIboolean\fR\fR] [\fB\-labeldirection\ \fR\fB\fIlist\fR\fR] [\fB\-treeangle\ \fR\fB\fIfloat\fR\fR] [\fB\-arc\ \fR\fB\fIfloat\fR\fR] \fB\-labelrotation\ \fR\fB\fIfloat\fR\fR [\fB\-rescaled\ \fR\fB\fItoggle\fR\fR] \fB\-bscale\ \fR\fB\fIfloat\fR\fR [\fB\-treedepth\ \fR\fB\fIfloat\fR\fR] \fB\-xmargin\ \fR\fB\fIfloat\fR\fR \fB\-ymargin\ \fR\fB\fIfloat\fR\fR \fB\-xrayshade\ \fR\fB\fIfloat\fR\fR \fB\-yrayshade\ \fR\fB\fIfloat\fR\fR [\fB\-paperx\ \fR\fB\fIfloat\fR\fR] [\fB\-papery\ \fR\fB\fIfloat\fR\fR] [\fB\-pagesheight\ \fR\fB\fIfloat\fR\fR] [\fB\-pageswidth\ \fR\fB\fIfloat\fR\fR] [\fB\-hpmargin\ \fR\fB\fIfloat\fR\fR] [\fB\-vpmargin\ \fR\fB\fIfloat\fR\fR] +.HP \w'\fBfdrawtree\fR\ 'u +\fBfdrawtree\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdrawtree\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Tree drawing" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-fontfile\fR \fIstring\fR +.RS 4 +Default value: font1 +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.SS "Output section" +.PP +\fB\-plotfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-plotter\fR \fIlist\fR +.RS 4 +Default value: l +.RE +.PP +\fB\-previewer\fR \fIlist\fR +.RS 4 +Default value: x +.RE +.PP +\fB\-iterate\fR \fIlist\fR +.RS 4 +Default value: e +.RE +.PP +\fB\-lengths\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-labeldirection\fR \fIlist\fR +.RS 4 +Default value: m +.RE +.PP +\fB\-treeangle\fR \fIfloat\fR +.RS 4 +Default value: 90\&.0 +.RE +.PP +\fB\-arc\fR \fIfloat\fR +.RS 4 +Default value: 360 +.RE +.PP +\fB\-labelrotation\fR \fIfloat\fR +.RS 4 +Default value: 90\&.0 +.RE +.PP +\fB\-rescaled\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-bscale\fR \fIfloat\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-treedepth\fR \fIfloat\fR +.RS 4 +Default value: 0\&.53 +.RE +.PP +\fB\-xmargin\fR \fIfloat\fR +.RS 4 +Default value: 1\&.65 +.RE +.PP +\fB\-ymargin\fR \fIfloat\fR +.RS 4 +Default value: 2\&.16 +.RE +.PP +\fB\-xrayshade\fR \fIfloat\fR +.RS 4 +Default value: 1\&.65 +.RE +.PP +\fB\-yrayshade\fR \fIfloat\fR +.RS 4 +Default value: 2\&.16 +.RE +.PP +\fB\-paperx\fR \fIfloat\fR +.RS 4 +Default value: 20\&.63750 +.RE +.PP +\fB\-papery\fR \fIfloat\fR +.RS 4 +Default value: 26\&.98750 +.RE +.PP +\fB\-pagesheight\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-pageswidth\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-hpmargin\fR \fIfloat\fR +.RS 4 +Default value: 0\&.41275 +.RE +.PP +\fB\-vpmargin\fR \fIfloat\fR +.RS 4 +Default value: 0\&.53975 +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdrawtree is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fseqbootall.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fseqbootall.1e @@ -0,0 +1,172 @@ +'\" t +.\" Title: FSEQBOOTALL +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FSEQBOOTALL" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fseqbootall \- Bootstrapped sequences algorithm +.SH "SYNOPSIS" +.HP \w'\fBfseqbootall\fR\ 'u +\fBfseqbootall\fR \fB\-infilesequences\ \fR\fB\fIseqset\fR\fR [\fB\-categories\ \fR\fB\fIproperties\fR\fR] [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] \fB\-datatype\ \fR\fB\fIlist\fR\fR \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-rewriteformat\ \fR\fB\fIlist\fR\fR \fB\-seqtype\ \fR\fB\fIlist\fR\fR \fB\-morphseqtype\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-enzymes\ \fR\fB\fIboolean\fR\fR \fB\-all\ \fR\fB\fIboolean\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfseqbootall\fR\ 'u +\fBfseqbootall\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfseqbootall\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infilesequences\fR \fIseqset\fR +.RS 4 +.RE +.PP +\fB\-categories\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-mixfile\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-ancfile\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file +.RE +.PP +\fB\-factorfile\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-datatype\fR \fIlist\fR +.RS 4 +Default value: s +.RE +.PP +\fB\-test\fR \fIlist\fR +.RS 4 +Default value: b +.RE +.PP +\fB\-regular\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-fracsample\fR \fIfloat\fR +.RS 4 +Default value: 100\&.0 +.RE +.PP +\fB\-rewriteformat\fR \fIlist\fR +.RS 4 +Default value: p +.RE +.PP +\fB\-seqtype\fR \fIlist\fR +.RS 4 +Default value: d +.RE +.PP +\fB\-morphseqtype\fR \fIlist\fR +.RS 4 +Default value: p +.RE +.PP +\fB\-blocksize\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-reps\fR \fIinteger\fR +.RS 4 +Default value: 100 +.RE +.PP +\fB\-justweights\fR \fIlist\fR +.RS 4 +Default value: d +.RE +.PP +\fB\-enzymes\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-all\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-dotdiff\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fseqbootall is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdollop.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdollop.1e @@ -0,0 +1,137 @@ +'\" t +.\" Title: FDOLLOP +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDOLLOP" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdollop \- Dollo and polymorphism parsimony algorithm +.SH "SYNOPSIS" +.HP \w'\fBfdollop\fR\ 'u +\fBfdollop\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-method\ \fR\fB\fIlist\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfdollop\fR\ 'u +\fBfdollop\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdollop\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIdiscretestates\fR +.RS 4 +File containing one or more data sets +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-ancfile\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: d +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: $(infile\&.discretesize) +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-ancseq\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-stepbox\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdollop is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fclique.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fclique.1e @@ -0,0 +1,120 @@ +'\" t +.\" Title: FCLIQUE +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FCLIQUE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fclique \- Largest clique program +.SH "SYNOPSIS" +.HP \w'\fBfclique\fR\ 'u +\fBfclique\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-cliqmin\ \fR\fB\fIinteger\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-printcomp\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfclique\fR\ 'u +\fBfclique\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfclique\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIdiscretestates\fR +.RS 4 +.RE +.PP +\fB\-ancfile\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-factorfile\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-cliqmin\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-printcomp\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fclique is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/frestboot.1e +++ embassy-phylip-3.69+20100721/debian/manpages/frestboot.1e @@ -0,0 +1,137 @@ +'\" t +.\" Title: FRESTBOOT +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FRESTBOOT" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +frestboot \- Bootstrapped restriction sites algorithm +.SH "SYNOPSIS" +.HP \w'\fBfrestboot\fR\ 'u +\fBfrestboot\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-rewriteformat\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR [\fB\-enzymes\ \fR\fB\fIboolean\fR\fR] \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfrestboot\fR\ 'u +\fBfrestboot\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfrestboot\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIdiscretestates\fR +.RS 4 +File containing one or more sets of restriction data +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file +.RE +.SS "Additional section" +.PP +\fB\-test\fR \fIlist\fR +.RS 4 +Default value: b +.RE +.PP +\fB\-regular\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-fracsample\fR \fIfloat\fR +.RS 4 +Default value: 100\&.0 +.RE +.PP +\fB\-rewriteformat\fR \fIlist\fR +.RS 4 +Default value: p +.RE +.PP +\fB\-blocksize\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-reps\fR \fIinteger\fR +.RS 4 +Default value: 100 +.RE +.PP +\fB\-justweights\fR \fIlist\fR +.RS 4 +Default value: d +.RE +.PP +\fB\-enzymes\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-dotdiff\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +frestboot is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fmove.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fmove.1e @@ -0,0 +1,118 @@ +'\" t +.\" Title: FMOVE +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FMOVE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fmove \- Interactive mixed method parsimony +.SH "SYNOPSIS" +.HP \w'\fBfmove\fR\ 'u +\fBfmove\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] [\fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR] +.HP \w'\fBfmove\fR\ 'u +\fBfmove\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfmove\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIdiscretestates\fR +.RS 4 +File containing data set +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file +.RE +.PP +\fB\-ancfile\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-factorfile\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: Wagner +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: $(infile\&.discretesize) +.RE +.PP +\fB\-initialtree\fR \fIlist\fR +.RS 4 +Default value: Arbitary +.RE +.PP +\fB\-screenwidth\fR \fIinteger\fR +.RS 4 +Default value: 80 +.RE +.PP +\fB\-screenlines\fR \fIinteger\fR +.RS 4 +Default value: 24 +.RE +.SS "Output section" +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fmove is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdrawgram.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdrawgram.1e @@ -0,0 +1,186 @@ +'\" t +.\" Title: FDRAWGRAM +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDRAWGRAM" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdrawgram \- Plots a cladogram\- or phenogram\-like rooted tree diagram +.SH "SYNOPSIS" +.HP \w'\fBfdrawgram\fR\ 'u +\fBfdrawgram\fR \fB\-fontfile\ \fR\fB\fIstring\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-plotfile\ \fR\fB\fIoutfile\fR\fR [\fB\-grows\ \fR\fB\fIboolean\fR\fR] [\fB\-style\ \fR\fB\fIlist\fR\fR] [\fB\-plotter\ \fR\fB\fIlist\fR\fR] [\fB\-previewer\ \fR\fB\fIlist\fR\fR] [\fB\-lengths\ \fR\fB\fIboolean\fR\fR] \fB\-labelrotation\ \fR\fB\fIfloat\fR\fR [\fB\-rescaled\ \fR\fB\fItoggle\fR\fR] \fB\-bscale\ \fR\fB\fIfloat\fR\fR [\fB\-treedepth\ \fR\fB\fIfloat\fR\fR] [\fB\-stemlength\ \fR\fB\fIfloat\fR\fR] [\fB\-nodespace\ \fR\fB\fIfloat\fR\fR] [\fB\-nodeposition\ \fR\fB\fIlist\fR\fR] \fB\-xmargin\ \fR\fB\fIfloat\fR\fR \fB\-ymargin\ \fR\fB\fIfloat\fR\fR \fB\-xrayshade\ \fR\fB\fIfloat\fR\fR \fB\-yrayshade\ \fR\fB\fIfloat\fR\fR [\fB\-paperx\ \fR\fB\fIfloat\fR\fR] [\fB\-papery\ \fR\fB\fIfloat\fR\fR] [\fB\-pagesheight\ \fR\fB\fIfloat\fR\fR] [\fB\-pageswidth\ \fR\fB\fIfloat\fR\fR] [\fB\-hpmargin\ \fR\fB\fIfloat\fR\fR] [\fB\-vpmargin\ \fR\fB\fIfloat\fR\fR] +.HP \w'\fBfdrawgram\fR\ 'u +\fBfdrawgram\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdrawgram\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Tree drawing" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-fontfile\fR \fIstring\fR +.RS 4 +Default value: font1 +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.SS "Output section" +.PP +\fB\-plotfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-grows\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-style\fR \fIlist\fR +.RS 4 +Default value: c +.RE +.PP +\fB\-plotter\fR \fIlist\fR +.RS 4 +Default value: l +.RE +.PP +\fB\-previewer\fR \fIlist\fR +.RS 4 +Default value: x +.RE +.PP +\fB\-lengths\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-labelrotation\fR \fIfloat\fR +.RS 4 +Default value: 90\&.0 +.RE +.PP +\fB\-rescaled\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-bscale\fR \fIfloat\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-treedepth\fR \fIfloat\fR +.RS 4 +Default value: 0\&.53 +.RE +.PP +\fB\-stemlength\fR \fIfloat\fR +.RS 4 +Default value: 0\&.05 +.RE +.PP +\fB\-nodespace\fR \fIfloat\fR +.RS 4 +Default value: 0\&.3333 +.RE +.PP +\fB\-nodeposition\fR \fIlist\fR +.RS 4 +Default value: c +.RE +.PP +\fB\-xmargin\fR \fIfloat\fR +.RS 4 +Default value: 1\&.65 +.RE +.PP +\fB\-ymargin\fR \fIfloat\fR +.RS 4 +Default value: 2\&.16 +.RE +.PP +\fB\-xrayshade\fR \fIfloat\fR +.RS 4 +Default value: 1\&.65 +.RE +.PP +\fB\-yrayshade\fR \fIfloat\fR +.RS 4 +Default value: 2\&.16 +.RE +.PP +\fB\-paperx\fR \fIfloat\fR +.RS 4 +Default value: 20\&.63750 +.RE +.PP +\fB\-papery\fR \fIfloat\fR +.RS 4 +Default value: 26\&.98750 +.RE +.PP +\fB\-pagesheight\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-pageswidth\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-hpmargin\fR \fIfloat\fR +.RS 4 +Default value: 0\&.41275 +.RE +.PP +\fB\-vpmargin\fR \fIfloat\fR +.RS 4 +Default value: 0\&.53975 +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdrawgram is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fprotdist.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fprotdist.1e @@ -0,0 +1,144 @@ +'\" t +.\" Title: FPROTDIST +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FPROTDIST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fprotdist \- Protein distance algorithm +.SH "SYNOPSIS" +.HP \w'\fBfprotdist\fR\ 'u +\fBfprotdist\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-gamma\ \fR\fB\fIlist\fR\fR \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-aacateg\ \fR\fB\fIlist\fR\fR \fB\-whichcode\ \fR\fB\fIlist\fR\fR \fB\-ease\ \fR\fB\fIfloat\fR\fR \fB\-ttratio\ \fR\fB\fIfloat\fR\fR \fB\-basefreq\ \fR\fB\fIarray\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfprotdist\fR\ 'u +\fBfprotdist\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfprotdist\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-ncategories\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-rate\fR \fIarray\fR +.RS 4 +.RE +.PP +\fB\-categories\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: j +.RE +.PP +\fB\-gamma\fR \fIlist\fR +.RS 4 +Default value: c +.RE +.PP +\fB\-gammacoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-invarcoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-aacateg\fR \fIlist\fR +.RS 4 +Default value: G +.RE +.PP +\fB\-whichcode\fR \fIlist\fR +.RS 4 +Default value: u +.RE +.PP +\fB\-ease\fR \fIfloat\fR +.RS 4 +Default value: 0\&.457 +.RE +.PP +\fB\-ttratio\fR \fIfloat\fR +.RS 4 +Default value: 2\&.0 +.RE +.PP +\fB\-basefreq\fR \fIarray\fR +.RS 4 +Default value: 0\&.25 0\&.25 0\&.25 0\&.25 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fprotdist is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/frestdist.1e +++ embassy-phylip-3.69+20100721/debian/manpages/frestdist.1e @@ -0,0 +1,117 @@ +'\" t +.\" Title: FRESTDIST +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FRESTDIST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +frestdist \- Distance matrix from restriction sites or fragments +.SH "SYNOPSIS" +.HP \w'\fBfrestdist\fR\ 'u +\fBfrestdist\fR \fB\-data\ \fR\fB\fIdiscretestates\fR\fR [\fB\-restsites\ \fR\fB\fIboolean\fR\fR] [\fB\-neili\ \fR\fB\fIboolean\fR\fR] \fB\-gamma\ \fR\fB\fIboolean\fR\fR \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR [\fB\-ttratio\ \fR\fB\fIfloat\fR\fR] [\fB\-sitelength\ \fR\fB\fIinteger\fR\fR] [\fB\-lower\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfrestdist\fR\ 'u +\fBfrestdist\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfrestdist\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-data\fR \fIdiscretestates\fR +.RS 4 +File containing one or more sets of restriction data +.RE +.SS "Additional section" +.PP +\fB\-restsites\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-neili\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-gamma\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-gammacoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-ttratio\fR \fIfloat\fR +.RS 4 +Default value: 2\&.0 +.RE +.PP +\fB\-sitelength\fR \fIinteger\fR +.RS 4 +Default value: 6 +.RE +.PP +\fB\-lower\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +frestdist is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/ftreedistpair.1e +++ embassy-phylip-3.69+20100721/debian/manpages/ftreedistpair.1e @@ -0,0 +1,104 @@ +'\" t +.\" Title: FTREEDISTPAIR +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FTREEDISTPAIR" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +ftreedistpair \- Distances between two sets of trees +.SH "SYNOPSIS" +.HP \w'\fBftreedistpair\fR\ 'u +\fBftreedistpair\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR \fB\-bintreefile\ \fR\fB\fItree\fR\fR [\fB\-dtype\ \fR\fB\fIlist\fR\fR] [\fB\-pairing\ \fR\fB\fIlist\fR\fR] [\fB\-style\ \fR\fB\fIlist\fR\fR] [\fB\-noroot\ \fR\fB\fIboolean\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBftreedistpair\fR\ 'u +\fBftreedistpair\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBftreedistpair\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Consensus" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-bintreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-dtype\fR \fIlist\fR +.RS 4 +Default value: b +.RE +.PP +\fB\-pairing\fR \fIlist\fR +.RS 4 +Default value: l +.RE +.PP +\fB\-style\fR \fIlist\fR +.RS 4 +Default value: v +.RE +.PP +\fB\-noroot\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +ftreedistpair is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fproml.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fproml.1e @@ -0,0 +1,211 @@ +'\" t +.\" Title: FPROML +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FPROML" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fproml \- Protein phylogeny by maximum likelihood +.SH "SYNOPSIS" +.HP \w'\fBfproml\fR\ 'u +\fBfproml\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-model\ \fR\fB\fIlist\fR\fR] [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-rough\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfproml\fR\ 'u +\fBfproml\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfproml\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-ncategories\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-rate\fR \fIarray\fR +.RS 4 +.RE +.PP +\fB\-categories\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file +.RE +.SS "Additional section" +.PP +\fB\-lengths\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-model\fR \fIlist\fR +.RS 4 +Default value: Jones\-Taylor\-Thornton +.RE +.PP +\fB\-gamma\fR \fIlist\fR +.RS 4 +Default value: Constant rate +.RE +.PP +\fB\-gammacoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-ngammacat\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-invarcoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-ninvarcat\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-invarfrac\fR \fIfloat\fR +.RS 4 +Default value: 0\&.0 +.RE +.PP +\fB\-nhmmcategories\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-hmmrates\fR \fIarray\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-hmmprobabilities\fR \fIarray\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-adjsite\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-lambda\fR \fIfloat\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-global\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-rough\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-hypstate\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fproml is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/ffitch.1e +++ embassy-phylip-3.69+20100721/debian/manpages/ffitch.1e @@ -0,0 +1,148 @@ +'\" t +.\" Title: FFITCH +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FFITCH" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +ffitch \- Fitch\-Margoliash and Least\-Squares Distance Methods +.SH "SYNOPSIS" +.HP \w'\fBffitch\fR\ 'u +\fBffitch\fR \fB\-datafile\ \fR\fB\fIdistances\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-matrixtype\ \fR\fB\fIlist\fR\fR] [\fB\-minev\ \fR\fB\fIboolean\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-power\ \fR\fB\fIfloat\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR \fB\-negallowed\ \fR\fB\fIboolean\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-replicates\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBffitch\fR\ 'u +\fBffitch\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBffitch\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Distance matrix" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-datafile\fR \fIdistances\fR +.RS 4 +File containing one or more distance matrices +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-matrixtype\fR \fIlist\fR +.RS 4 +Default value: s +.RE +.PP +\fB\-minev\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-power\fR \fIfloat\fR +.RS 4 +Default value: 2\&.0 +.RE +.PP +\fB\-lengths\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-negallowed\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-global\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-replicates\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +ffitch is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdolmove.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdolmove.1e @@ -0,0 +1,119 @@ +'\" t +.\" Title: FDOLMOVE +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDOLMOVE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdolmove \- Interactive Dollo or Polymorphism Parsimony +.SH "SYNOPSIS" +.HP \w'\fBfdolmove\fR\ 'u +\fBfdolmove\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] [\fB\-method\ \fR\fB\fIlist\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] [\fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR] +.HP \w'\fBfdolmove\fR\ 'u +\fBfdolmove\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdolmove\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIdiscretestates\fR +.RS 4 +File containing data set +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file +.RE +.PP +\fB\-ancfile\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-factorfile\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: d +.RE +.PP +\fB\-thresh\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-initialtree\fR \fIlist\fR +.RS 4 +Default value: Arbitary +.RE +.PP +\fB\-screenwidth\fR \fIinteger\fR +.RS 4 +Default value: 80 +.RE +.PP +\fB\-screenlines\fR \fIinteger\fR +.RS 4 +Default value: 24 +.RE +.SS "Output section" +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdolmove is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdiscboot.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdiscboot.1e @@ -0,0 +1,155 @@ +'\" t +.\" Title: FDISCBOOT +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDISCBOOT" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdiscboot \- Bootstrapped discrete sites algorithm +.SH "SYNOPSIS" +.HP \w'\fBfdiscboot\fR\ 'u +\fBfdiscboot\fR \fB\-infile\ \fR\fB\fIdiscretestates\fR\fR [\fB\-mixfile\ \fR\fB\fIproperties\fR\fR] [\fB\-ancfile\ \fR\fB\fIproperties\fR\fR] [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-factorfile\ \fR\fB\fIproperties\fR\fR] \fB\-test\ \fR\fB\fIlist\fR\fR \fB\-regular\ \fR\fB\fItoggle\fR\fR \fB\-fracsample\ \fR\fB\fIfloat\fR\fR \fB\-morphseqtype\ \fR\fB\fIlist\fR\fR \fB\-blocksize\ \fR\fB\fIinteger\fR\fR \fB\-reps\ \fR\fB\fIinteger\fR\fR \fB\-justweights\ \fR\fB\fIlist\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outancfile\ \fR\fB\fIoutfile\fR\fR \fB\-outmixfile\ \fR\fB\fIoutfile\fR\fR \fB\-outfactfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfdiscboot\fR\ 'u +\fBfdiscboot\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdiscboot\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIdiscretestates\fR +.RS 4 +.RE +.PP +\fB\-mixfile\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-ancfile\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file +.RE +.PP +\fB\-factorfile\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-test\fR \fIlist\fR +.RS 4 +Default value: b +.RE +.PP +\fB\-regular\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-fracsample\fR \fIfloat\fR +.RS 4 +Default value: 100\&.0 +.RE +.PP +\fB\-morphseqtype\fR \fIlist\fR +.RS 4 +Default value: p +.RE +.PP +\fB\-blocksize\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-reps\fR \fIinteger\fR +.RS 4 +Default value: 100 +.RE +.PP +\fB\-justweights\fR \fIlist\fR +.RS 4 +Default value: d +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-outancfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-outmixfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-outfactfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-dotdiff\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdiscboot is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fprotpars.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fprotpars.1e @@ -0,0 +1,147 @@ +'\" t +.\" Title: FPROTPARS +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FPROTPARS" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fprotpars \- Protein parsimony algorithm +.SH "SYNOPSIS" +.HP \w'\fBfprotpars\fR\ 'u +\fBfprotpars\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-whichcode\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR +.HP \w'\fBfprotpars\fR\ 'u +\fBfprotpars\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfprotpars\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-thresh\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-whichcode\fR \fIlist\fR +.RS 4 +Default value: Universal +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-stepbox\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-ancseq\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-dotdiff\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fprotpars is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fkitsch.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fkitsch.1e @@ -0,0 +1,134 @@ +'\" t +.\" Title: FKITSCH +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FKITSCH" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fkitsch \- Fitch\-Margoliash method with contemporary tips +.SH "SYNOPSIS" +.HP \w'\fBfkitsch\fR\ 'u +\fBfkitsch\fR \fB\-datafile\ \fR\fB\fIdistances\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-matrixtype\ \fR\fB\fIlist\fR\fR] [\fB\-minev\ \fR\fB\fIboolean\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-power\ \fR\fB\fIfloat\fR\fR] [\fB\-negallowed\ \fR\fB\fIboolean\fR\fR] [\fB\-replicates\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfkitsch\fR\ 'u +\fBfkitsch\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfkitsch\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Distance matrix" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-datafile\fR \fIdistances\fR +.RS 4 +File containing one or more distance matrices +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-matrixtype\fR \fIlist\fR +.RS 4 +Default value: s +.RE +.PP +\fB\-minev\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-power\fR \fIfloat\fR +.RS 4 +Default value: 2\&.0 +.RE +.PP +\fB\-negallowed\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-replicates\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fkitsch is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdnapars.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdnapars.1e @@ -0,0 +1,162 @@ +'\" t +.\" Title: FDNAPARS +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDNAPARS" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdnapars \- DNA parsimony algorithm +.SH "SYNOPSIS" +.HP \w'\fBfdnapars\fR\ 'u +\fBfdnapars\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-maxtrees\ \fR\fB\fIinteger\fR\fR] \fB\-thorough\ \fR\fB\fItoggle\fR\fR \fB\-rearrange\ \fR\fB\fIboolean\fR\fR [\fB\-transversion\ \fR\fB\fIboolean\fR\fR] \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR +.HP \w'\fBfdnapars\fR\ 'u +\fBfdnapars\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdnapars\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-maxtrees\fR \fIinteger\fR +.RS 4 +Default value: 10000 +.RE +.PP +\fB\-thorough\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-rearrange\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-transversion\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-thresh\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: 1\&.0 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-stepbox\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-ancseq\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-dotdiff\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdnapars is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdnainvar.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdnainvar.1e @@ -0,0 +1,100 @@ +'\" t +.\" Title: FDNAINVAR +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDNAINVAR" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdnainvar \- Nucleic acid sequence Invariants method +.SH "SYNOPSIS" +.HP \w'\fBfdnainvar\fR\ 'u +\fBfdnainvar\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-weights\ \fR\fB\fIproperties\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] \fB\-dotdiff\ \fR\fB\fIboolean\fR\fR [\fB\-printpattern\ \fR\fB\fIboolean\fR\fR] [\fB\-printinvariant\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfdnainvar\fR\ 'u +\fBfdnainvar\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdnainvar\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-dotdiff\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-printpattern\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-printinvariant\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdnainvar is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/ffactor.1e +++ embassy-phylip-3.69+20100721/debian/manpages/ffactor.1e @@ -0,0 +1,94 @@ +'\" t +.\" Title: FFACTOR +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FFACTOR" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +ffactor \- Multistate to binary recoding program +.SH "SYNOPSIS" +.HP \w'\fBffactor\fR\ 'u +\fBffactor\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-anc\ \fR\fB\fIboolean\fR\fR] [\fB\-factors\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outfactorfile\ \fR\fB\fIoutfile\fR\fR \fB\-outancfile\ \fR\fB\fIoutfile\fR\fR +.HP \w'\fBffactor\fR\ 'u +\fBffactor\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBffactor\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Discrete characters" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIinfile\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-anc\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-factors\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-outfactorfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-outancfile\fR \fIoutfile\fR +.RS 4 +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +ffactor is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdnaml.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdnaml.1e @@ -0,0 +1,221 @@ +'\" t +.\" Title: FDNAML +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDNAML" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdnaml \- Estimates nucleotide phylogeny by maximum likelihood +.SH "SYNOPSIS" +.HP \w'\fBfdnaml\fR\ 'u +\fBfdnaml\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-ttratio\ \fR\fB\fIfloat\fR\fR] [\fB\-freqsfrom\ \fR\fB\fItoggle\fR\fR] \fB\-basefreq\ \fR\fB\fIarray\fR\fR [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-rough\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfdnaml\fR\ 'u +\fBfdnaml\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdnaml\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-ncategories\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-rate\fR \fIarray\fR +.RS 4 +.RE +.PP +\fB\-categories\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file +.RE +.SS "Additional section" +.PP +\fB\-lengths\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-ttratio\fR \fIfloat\fR +.RS 4 +Default value: 2\&.0 +.RE +.PP +\fB\-freqsfrom\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-basefreq\fR \fIarray\fR +.RS 4 +Default value: 0\&.25 0\&.25 0\&.25 0\&.25 +.RE +.PP +\fB\-gamma\fR \fIlist\fR +.RS 4 +Default value: Constant rate +.RE +.PP +\fB\-gammacoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-ngammacat\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-invarcoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-ninvarcat\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-invarfrac\fR \fIfloat\fR +.RS 4 +Default value: 0\&.0 +.RE +.PP +\fB\-nhmmcategories\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-hmmrates\fR \fIarray\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-hmmprobabilities\fR \fIarray\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-adjsite\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-lambda\fR \fIfloat\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-global\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-rough\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-hypstate\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdnaml is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fneighbor.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fneighbor.1e @@ -0,0 +1,124 @@ +'\" t +.\" Title: FNEIGHBOR +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FNEIGHBOR" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fneighbor \- Phylogenies from distance matrix by N\-J or UPGMA method +.SH "SYNOPSIS" +.HP \w'\fBfneighbor\fR\ 'u +\fBfneighbor\fR \fB\-datafile\ \fR\fB\fIdistances\fR\fR [\fB\-matrixtype\ \fR\fB\fIlist\fR\fR] [\fB\-treetype\ \fR\fB\fIlist\fR\fR] \fB\-outgrno\ \fR\fB\fIinteger\fR\fR [\fB\-jumble\ \fR\fB\fItoggle\fR\fR] \fB\-seed\ \fR\fB\fIinteger\fR\fR [\fB\-replicates\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfneighbor\fR\ 'u +\fBfneighbor\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfneighbor\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Distance matrix" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-datafile\fR \fIdistances\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-matrixtype\fR \fIlist\fR +.RS 4 +Default value: s +.RE +.PP +\fB\-treetype\fR \fIlist\fR +.RS 4 +Default value: n +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-jumble\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-replicates\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fneighbor is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fcontml.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fcontml.1e @@ -0,0 +1,128 @@ +'\" t +.\" Title: FCONTML +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FCONTML" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fcontml \- Gene frequency and continuous character Maximum Likelihood +.SH "SYNOPSIS" +.HP \w'\fBfcontml\fR\ 'u +\fBfcontml\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-datatype\ \fR\fB\fIlist\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfcontml\fR\ 'u +\fBfcontml\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfcontml\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Gene frequencies" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIfrequencies\fR +.RS 4 +File containing one or more sets of data +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-datatype\fR \fIlist\fR +.RS 4 +Default value: g +.RE +.PP +\fB\-lengths\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-global\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fcontml is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fconsense.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fconsense.1e @@ -0,0 +1,114 @@ +'\" t +.\" Title: FCONSENSE +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FCONSENSE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fconsense \- Majority\-rule and strict consensus tree +.SH "SYNOPSIS" +.HP \w'\fBfconsense\fR\ 'u +\fBfconsense\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-method\ \fR\fB\fIlist\fR\fR] \fB\-mlfrac\ \fR\fB\fIfloat\fR\fR [\fB\-root\ \fR\fB\fItoggle\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-prntsets\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfconsense\fR\ 'u +\fBfconsense\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfconsense\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Consensus" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: mre +.RE +.PP +\fB\-mlfrac\fR \fIfloat\fR +.RS 4 +Default value: 0\&.5 +.RE +.PP +\fB\-root\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-prntsets\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fconsense is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fgendist.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fgendist.1e @@ -0,0 +1,87 @@ +'\" t +.\" Title: FGENDIST +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FGENDIST" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fgendist \- Compute genetic distances from gene frequencies +.SH "SYNOPSIS" +.HP \w'\fBfgendist\fR\ 'u +\fBfgendist\fR \fB\-infile\ \fR\fB\fIfrequencies\fR\fR \fB\-method\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-lower\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfgendist\fR\ 'u +\fBfgendist\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfgendist\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Gene frequencies" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-infile\fR \fIfrequencies\fR +.RS 4 +File containing one or more sets of data +.RE +.SS "Additional section" +.PP +\fB\-method\fR \fIlist\fR +.RS 4 +Default value: n +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-lower\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fgendist is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdnamove.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdnamove.1e @@ -0,0 +1,109 @@ +'\" t +.\" Title: FDNAMOVE +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDNAMOVE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdnamove \- Interactive DNA parsimony +.SH "SYNOPSIS" +.HP \w'\fBfdnamove\fR\ 'u +\fBfdnamove\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] [\fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR] +.HP \w'\fBfdnamove\fR\ 'u +\fBfdnamove\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdnamove\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +Weights file \- ignore sites with weight zero +.RE +.SS "Additional section" +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-thresh\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-initialtree\fR \fIlist\fR +.RS 4 +Default value: Arbitary +.RE +.PP +\fB\-screenwidth\fR \fIinteger\fR +.RS 4 +Default value: 80 +.RE +.PP +\fB\-screenlines\fR \fIinteger\fR +.RS 4 +Default value: 24 +.RE +.SS "Output section" +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdnamove is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fpromlk.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fpromlk.1e @@ -0,0 +1,205 @@ +'\" t +.\" Title: FPROMLK +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FPROMLK" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fpromlk \- Protein phylogeny by maximum likelihood +.SH "SYNOPSIS" +.HP \w'\fBfpromlk\fR\ 'u +\fBfpromlk\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-ncategories\ \fR\fB\fIinteger\fR\fR] \fB\-rate\ \fR\fB\fIarray\fR\fR \fB\-categories\ \fR\fB\fIproperties\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] \fB\-lengths\ \fR\fB\fIboolean\fR\fR [\fB\-model\ \fR\fB\fIlist\fR\fR] [\fB\-gamma\ \fR\fB\fIlist\fR\fR] \fB\-gammacoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ngammacat\ \fR\fB\fIinteger\fR\fR \fB\-invarcoefficient\ \fR\fB\fIfloat\fR\fR \fB\-ninvarcat\ \fR\fB\fIinteger\fR\fR \fB\-invarfrac\ \fR\fB\fIfloat\fR\fR \fB\-nhmmcategories\ \fR\fB\fIinteger\fR\fR \fB\-hmmrates\ \fR\fB\fIarray\fR\fR \fB\-hmmprobabilities\ \fR\fB\fIarray\fR\fR \fB\-adjsite\ \fR\fB\fIboolean\fR\fR \fB\-lambda\ \fR\fB\fIfloat\fR\fR \fB\-njumble\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-global\ \fR\fB\fIboolean\fR\fR [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-hypstate\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfpromlk\fR\ 'u +\fBfpromlk\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfpromlk\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.PP +\fB\-ncategories\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-rate\fR \fIarray\fR +.RS 4 +.RE +.PP +\fB\-categories\fR \fIproperties\fR +.RS 4 +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-lengths\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-model\fR \fIlist\fR +.RS 4 +Default value: Jones\-Taylor\-Thornton +.RE +.PP +\fB\-gamma\fR \fIlist\fR +.RS 4 +Default value: n +.RE +.PP +\fB\-gammacoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-ngammacat\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-invarcoefficient\fR \fIfloat\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-ninvarcat\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-invarfrac\fR \fIfloat\fR +.RS 4 +Default value: 0\&.0 +.RE +.PP +\fB\-nhmmcategories\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-hmmrates\fR \fIarray\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-hmmprobabilities\fR \fIarray\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-adjsite\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-lambda\fR \fIfloat\fR +.RS 4 +Default value: 1\&.0 +.RE +.PP +\fB\-njumble\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-seed\fR \fIinteger\fR +.RS 4 +Default value: 1 +.RE +.PP +\fB\-global\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-hypstate\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fpromlk is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fdnapenny.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fdnapenny.1e @@ -0,0 +1,139 @@ +'\" t +.\" Title: FDNAPENNY +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FDNAPENNY" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fdnapenny \- Penny algorithm for DNA +.SH "SYNOPSIS" +.HP \w'\fBfdnapenny\fR\ 'u +\fBfdnapenny\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR [\fB\-weights\ \fR\fB\fIproperties\fR\fR] [\fB\-howoften\ \fR\fB\fIinteger\fR\fR] [\fB\-howmany\ \fR\fB\fIinteger\fR\fR] [\fB\-simple\ \fR\fB\fIboolean\fR\fR] [\fB\-outgrno\ \fR\fB\fIinteger\fR\fR] [\fB\-thresh\ \fR\fB\fItoggle\fR\fR] \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-trout\ \fR\fB\fItoggle\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR [\fB\-printdata\ \fR\fB\fIboolean\fR\fR] [\fB\-progress\ \fR\fB\fIboolean\fR\fR] [\fB\-treeprint\ \fR\fB\fIboolean\fR\fR] [\fB\-stepbox\ \fR\fB\fIboolean\fR\fR] [\fB\-ancseq\ \fR\fB\fIboolean\fR\fR] +.HP \w'\fBfdnapenny\fR\ 'u +\fBfdnapenny\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfdnapenny\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-sequence\fR \fIseqsetall\fR +.RS 4 +File containing one or more sequence alignments +.RE +.PP +\fB\-weights\fR \fIproperties\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-howoften\fR \fIinteger\fR +.RS 4 +Default value: 100 +.RE +.PP +\fB\-howmany\fR \fIinteger\fR +.RS 4 +Default value: 1000 +.RE +.PP +\fB\-simple\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outgrno\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-thresh\fR \fItoggle\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-threshold\fR \fIfloat\fR +.RS 4 +Default value: 1\&.0 +.RE +.SS "Output section" +.PP +\fB\-outfile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-trout\fR \fItoggle\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.PP +\fB\-printdata\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-progress\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-treeprint\fR \fIboolean\fR +.RS 4 +Default value: Y +.RE +.PP +\fB\-stepbox\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.PP +\fB\-ancseq\fR \fIboolean\fR +.RS 4 +Default value: N +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fdnapenny is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp --- embassy-phylip-3.69+20100721.orig/debian/manpages/fretree.1e +++ embassy-phylip-3.69+20100721/debian/manpages/fretree.1e @@ -0,0 +1,100 @@ +'\" t +.\" Title: FRETREE +.\" Author: Debian Med Packaging Team +.\" Generator: DocBook XSL Stylesheets v1.75.2 +.\" Date: 08/11/2010 +.\" Manual: EMBOSS Manual for Debian +.\" Source: PHYLIPNEW 3.69+20100721 +.\" Language: English +.\" +.TH "FRETREE" "1e" "08/11/2010" "PHYLIPNEW 3.69+20100721" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +fretree \- Interactive tree rearrangement +.SH "SYNOPSIS" +.HP \w'\fBfretree\fR\ 'u +\fBfretree\fR \fB\-spp\ \fR\fB\fIinteger\fR\fR \fB\-intreefile\ \fR\fB\fItree\fR\fR [\fB\-initialtree\ \fR\fB\fIlist\fR\fR] [\fB\-format\ \fR\fB\fIlist\fR\fR] [\fB\-screenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-vscreenwidth\ \fR\fB\fIinteger\fR\fR] [\fB\-screenlines\ \fR\fB\fIinteger\fR\fR] \fB\-outtreefile\ \fR\fB\fIoutfile\fR\fR +.HP \w'\fBfretree\fR\ 'u +\fBfretree\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBfretree\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Tree drawing" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-spp\fR \fIinteger\fR +.RS 4 +.RE +.PP +\fB\-intreefile\fR \fItree\fR +.RS 4 +.RE +.SS "Additional section" +.PP +\fB\-initialtree\fR \fIlist\fR +.RS 4 +Default value: Arbitary +.RE +.PP +\fB\-format\fR \fIlist\fR +.RS 4 +Default value: p +.RE +.PP +\fB\-screenwidth\fR \fIinteger\fR +.RS 4 +Default value: 80 +.RE +.PP +\fB\-vscreenwidth\fR \fIinteger\fR +.RS 4 +Default value: 80 +.RE +.PP +\fB\-screenlines\fR \fIinteger\fR +.RS 4 +Default value: 24 +.RE +.SS "Output section" +.PP +\fB\-outtreefile\fR \fIoutfile\fR +.RS 4 +.RE +.SH "BUGS" +.PP +Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. +.SH "SEE ALSO" +.PP +fretree is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +.PP +This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. +.sp