debian/0000755000000000000000000000000012200742217007163 5ustar debian/phylip-doc.links0000644000000000000000000000023211110210221012252 0ustar usr/share/doc/phylip/html/phylip.html usr/share/doc/phylip/html/index.html usr/share/doc/phylip/html/doc/main.html usr/share/doc/phylip/html/index.html debian/phylip-doc.doc-base0000644000000000000000000000121211110210221012606 0ustar Document: phylip-doc Title: Phylip 3.66 (Manual) Author: Joe Felsenstein Abstract: Phylogeny Inference Package The PHYLogeny Inference Package is a package of programs for inferring phylogenies (evolutionary trees) from sequences. 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, distance matrices, and 0/1 discrete characters. Section: Science/Biology Format: html Index: /usr/share/doc/phylip/html/index.html Files: /usr/share/doc/phylip/html/* debian/source/0000755000000000000000000000000012200737610010464 5ustar debian/source/lintian-overrides0000644000000000000000000000034412200737610014046 0ustar # The package is non-free anyway - so why bothering touching the source phylip: source-contains-prebuilt-windows-binary src/javajars/DrawGramJava.exe phylip: source-contains-prebuilt-windows-binary src/javajars/DrawTreeJava.exe debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/README.source0000644000000000000000000000026711246743457011367 0ustar This packages uses the quilt patch system. Please read /usr/share/doc/quilt/README.source for more information. -- Andreas Tille Mon, 31 Aug 2009 14:50:19 +0200 debian/copyright0000644000000000000000000000310611110210221011076 0ustar This package was debianized by Andreas Tille on Tue, 30 Oct 2001 07:09:09 +0100 It was downloaded from ftp://evolution.genetics.washington.edu/pub/phylip The home page is: http://evolution.genetics.washington.edu/phylip.html Further Information on: http://evolution.genetics.washington.edu/phylip/software.html Upstream author: Joe Felsenstein http://evolution.genetics.washington.edu/phylip/felsenstein.html Copyright Notice for PHYLIP http://evolution.genetics.washington.edu/phylip/doc/main.html#copyright The following copyright notice is intended to cover all source code, all documentation, and all executable programs of the PHYLIP package. © Copyright 1980-2004. University of Washington and Joseph Felsenstein. All rights reserved. Permission is granted to reproduce, perform, and modify these programs and documentation files. Permission is granted to distribute or provide access to these programs provided that this copyright notice is not removed, the programs are not integrated with or called by any product or service that generates revenue, and that your distribution of these documentation files and programs are free. Any modified versions of these materials that are distributed or accessible shall indicate that they are based on these program. Institutions of higher education are granted permission to distribute this material to their students and staff for a fee to recover distribution costs. Permission requests for any other distribution of this program should be directed to license @ u.washington.edu . debian/phylip.manpages0000644000000000000000000000002011110210221012155 0ustar debian/phylip.1 debian/rules0000755000000000000000000000112312200730071010233 0ustar #!/usr/bin/make -f # debian/rules for phylip using dh # Andreas Tille , GPL %: dh $@ override_dh_auto_build: dh_auto_build --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx all override_dh_auto_install: dh_auto_install --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx install DATADIR=../fonts override_dh_installexamples: dh_installexamples find debian -type f -name "*.txt" -exec chmod a-x \{\} \; override_dh_auto_clean: dh_auto_clean --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx clean rm -fr exe/* fonts/ src/*.so debian/phylip.lintian-overrides0000644000000000000000000001253212200737520014054 0ustar # Seems to be false positives - options are properly set phylip: hardening-no-fortify-functions usr/lib/phylip/bin/clique phylip: hardening-no-fortify-functions usr/lib/phylip/bin/consense phylip: hardening-no-fortify-functions usr/lib/phylip/bin/contml phylip: hardening-no-fortify-functions usr/lib/phylip/bin/contrast phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnacomp phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnadist phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnainvar phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnaml phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnamlk phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnamove phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnapars phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dnapenny phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dollop phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dolmove phylip: hardening-no-fortify-functions usr/lib/phylip/bin/dolpenny phylip: hardening-no-fortify-functions usr/lib/phylip/bin/drawgram phylip: hardening-no-fortify-functions usr/lib/phylip/bin/drawtree phylip: hardening-no-fortify-functions usr/lib/phylip/bin/factor phylip: hardening-no-fortify-functions usr/lib/phylip/bin/fitch phylip: hardening-no-fortify-functions usr/lib/phylip/bin/gendist phylip: hardening-no-fortify-functions usr/lib/phylip/bin/kitsch phylip: hardening-no-fortify-functions usr/lib/phylip/bin/libdrawgram.so phylip: hardening-no-fortify-functions usr/lib/phylip/bin/libdrawtree.so phylip: hardening-no-fortify-functions usr/lib/phylip/bin/mix phylip: hardening-no-fortify-functions usr/lib/phylip/bin/move phylip: hardening-no-fortify-functions usr/lib/phylip/bin/neighbor phylip: hardening-no-fortify-functions usr/lib/phylip/bin/pars phylip: hardening-no-fortify-functions usr/lib/phylip/bin/penny phylip: hardening-no-fortify-functions usr/lib/phylip/bin/proml phylip: hardening-no-fortify-functions usr/lib/phylip/bin/promlk phylip: hardening-no-fortify-functions usr/lib/phylip/bin/protdist phylip: hardening-no-fortify-functions usr/lib/phylip/bin/protpars phylip: hardening-no-fortify-functions usr/lib/phylip/bin/restdist phylip: hardening-no-fortify-functions usr/lib/phylip/bin/restml phylip: hardening-no-fortify-functions usr/lib/phylip/bin/retree phylip: hardening-no-fortify-functions usr/lib/phylip/bin/seqboot phylip: hardening-no-fortify-functions usr/lib/phylip/bin/treedist # No idea why upstream is providing duplicated files - they are small in any case phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dollop/dollopinfile.txt usr/share/doc/phylip/examples/testdata/mix/mixinfile.txt usr/share/doc/phylip/examples/testdata/pars/parsinfile.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/fitch/fitchinfile.txt usr/share/doc/phylip/examples/testdata/kitsch/kitschinfile.txt usr/share/doc/phylip/examples/testdata/neighbor/neighborinfile.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnacomp/dnacompinfile.txt usr/share/doc/phylip/examples/testdata/dnapars/dnaparsinfile.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/mammal.txt usr/share/doc/phylip/examples/testdata/drawtree/mammal.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/14tip.txt usr/share/doc/phylip/examples/testdata/drawtree/14tip.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlcats.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkcats.txt usr/share/doc/phylip/examples/testdata/proml/promlcats.txt usr/share/doc/phylip/examples/testdata/promlk/promlkcats.txt usr/share/doc/phylip/examples/testdata/protdist/protdistcats.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/ape2.txt usr/share/doc/phylip/examples/testdata/drawtree/ape2.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlweights.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkweights.txt usr/share/doc/phylip/examples/testdata/proml/promlweights.txt usr/share/doc/phylip/examples/testdata/promlk/promlkweights.txt usr/share/doc/phylip/examples/testdata/protdist/protdistweights.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/contml/contmlinfile.txt usr/share/doc/phylip/examples/testdata/gendist/gendistinfile.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlinfile.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkinfile.txt usr/share/doc/phylip/examples/testdata/proml/promlinfile.txt usr/share/doc/phylip/examples/testdata/promlk/promlkinfile.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/restdist/restdistoutfile.txt usr/share/doc/phylip/examples/testdata/restml/restmloutfile.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/clique/cliqueinfile.txt usr/share/doc/phylip/examples/testdata/dolmove/dolmoveinfile.txt usr/share/doc/phylip/examples/testdata/move/moveinfile.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/cats.txt usr/share/doc/phylip/examples/testdata/drawtree/cats.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/ape1.txt usr/share/doc/phylip/examples/testdata/drawtree/ape1.txt phylip: duplicate-files usr/share/doc/phylip/examples/testdata/restdist/restdistinfile.txt usr/share/doc/phylip/examples/testdata/restml/restmlinfile.txt debian/phylip.examples0000644000000000000000000000003612200727535012235 0ustar debian/examples/* src/testdatadebian/patches/0000755000000000000000000000000012200742034010607 5ustar debian/patches/01_src_phylip_h0000644000000000000000000000112312200631420013506 0ustar Author: Andreas Tille Forwarded: No Description: Debian keeps the font files in a different location than normal installer License: see debian/copyright --- a/src/phylip.h +++ b/src/phylip.h @@ -72,7 +72,7 @@ void phyFillScreenColor(void); #define EBCDIC false #define INFILE "infile" #define OUTFILE "outfile" -#define FONTFILE "fontfile" /* on unix this might be /usr/local/lib/fontfile */ +#define FONTFILE "/usr/share/phylip/fontfile" /* on unix this might be /usr/local/lib/fontfile */ #define PLOTFILE "plotfile" #define INTREE "intree" #define INTREE2 "intree2" debian/patches/hardening.patch0000644000000000000000000000235612200742034013575 0ustar Author: Andreas Tille LastChanged: Wed, 07 Aug 2013 22:17:03 +0200 Description: Let hardening flags sneek in --- a/src/Makefile.unx +++ b/src/Makefile.unx @@ -126,7 +126,7 @@ DFLAGS = $(CFLAGS) # # Most of the programs need only the math libraries, specified like this; # -LIBS = -lm +LIBS = -lm $(LDFLAGS) # # The drawing programs may also need access to the graphics libraries. This is # specified with the DLIBS variable. @@ -380,7 +380,7 @@ drawgram: drawgram.o draw.o draw2.o # needed by java libdrawgram.so: drawgram.o draw.o draw2.o phylip.o - $(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) + $(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) $(LDFLAGS) drawtree.o: drawtree.c draw.h phylip.h $(CC) $(DFLAGS) -shared -fPIC -c drawtree.c @@ -390,7 +390,7 @@ drawtree: drawtree.o draw.o draw2.o # needed by java libdrawtree.so: drawtree.o draw.o draw2.o phylip.o - $(CC) $(CFLAGS) -o libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) + $(CC) $(CFLAGS) -o libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) $(LDFLAGS) factor.o: factor.c phylip.h debian/patches/series0000644000000000000000000000007112200734757012037 0ustar install_fonts_data.patch hardening.patch 01_src_phylip_h debian/patches/install_fonts_data.patch0000644000000000000000000000232412200705376015511 0ustar Author: Andreas Tille Forwarded: No Description: Debian keeps the font files in a different location than normal installer; distclean target makes sure everything will be cleaned up --- a/src/Makefile.unx +++ b/src/Makefile.unx @@ -51,6 +51,7 @@ VERSION=3.695 # # the following specifies the directory where the executables will be placed EXEDIR = ../exe +DATADIR = ../exe # # ---------------------------------------------------------------------------- # @@ -235,8 +236,10 @@ put: @cp $(DYLIBS) $(EXEDIR) @echo "Installing jar files in $(EXEDIR)" @cp $(JARS) $(EXEDIR) - @echo "Installing font files in $(EXEDIR)" - @cp font* $(EXEDIR) + @echo "Installing font files in $(DATADIR)" + @mkdir -p $(DATADIR) + @cp font* $(DATADIR) + @cd $(DATADIR) && ln -s font1 fontfile @echo "Copying testdata files to $(EXEDIR)/testdata/..." mkdir $(EXEDIR)/testdata for i in $(TESTDIR); do \ @@ -259,6 +262,12 @@ clean: @echo "Finished cleanup." @echo "" +distclean: clean + @echo "Removing executables" + @rm -rf $(EXEDIR) $(DATADIR) + @echo "Finaly removed all executable files." + @echo "" + # # compile object files shared between programs # (make's implicit rule for %.o will take care of these) debian/phylip.install0000644000000000000000000000017212200727477012073 0ustar exe/[a-su-z]* usr/lib/phylip/bin exe/t[a-df-z]* usr/lib/phylip/bin fonts/* usr/share/phylip debian/bin/phylip usr/bin debian/README.debian0000644000000000000000000000150311110210221011243 0ustar phylip for DEBIAN ---------------------- Because Phylip is made of several different programs, some of which having names which conflict with other Unix programs (like "factor"), the Debian installation uses a wrapper, named "phylip", which is used to invoke the specific programs. So, to run dnapenny, you type: phylip dnapenny If it bothers you, just add "/usr/lib/phylip/bin" in front of your PATH and you'll get the Phylip programs as usual. Test files and samples are in /usr/share/doc/phylip/examples/tests. Just type make. The reference Web site is: http://evolution.genetics.washington.edu/phylip.html The original packaging was done by: Dr. Guenter Bechly , Sat, 7 Apr 2001 16:00:14 +0200 The current Debian Maintainer is: Andreas Tille Tue, 23 Oct 2001 12:35:14 +0200 debian/phylip-doc.install0000644000000000000000000000010611110210221012600 0ustar doc usr/share/doc/phylip/html phylip.* usr/share/doc/phylip/html debian/watch0000644000000000000000000000012311243336530010213 0ustar version=3 http://evolution.gs.washington.edu/phylip/download/phylip-(.*)\.tar\.gz debian/bin/0000755000000000000000000000000012200530436007731 5ustar debian/bin/phylip0000644000000000000000000000062411110210221011145 0ustar #!/bin/sh BINDIR=/usr/lib/phylip/bin if [ $# -lt 1 ] ; then echo "Usage: $0 " 1>&2 echo " Existing programs are:" ls ${BINDIR} exit 1 fi WRAPPER=$0 PROGRAM=$1 shift ARGS=$* if [ -x ${BINDIR}/${PROGRAM} ]; then exec ${BINDIR}/${PROGRAM} ${ARGS} else echo "Usage: ${PROGRAM} does not exist in Phylip" echo " Existing programs are:" ls ${BINDIR} exit 1 fi debian/changelog0000644000000000000000000001460012200741615011037 0ustar phylip (1:3.695-1) unstable; urgency=low * New upstream version * debian/control: - use anonscm in Vcs fields - cme fix dpkg-control - debhelper 9 - debian/source/format: 3.0 (quilt) * Upstream changed build system - this chance was used to switch from cdbs to dh (patches were changed) * Lintian overrides -- Andreas Tille Wed, 07 Aug 2013 22:17:03 +0200 phylip (1:3.69-1) unstable; urgency=low * New upstream release * debian/control: - Fixed Vcs-Svn (missing svn/) - Updated Standards-Version to 3.8.3 (README.source) - Droped [Biology] from short description * Debhelper 7 -- Andreas Tille Fri, 11 Sep 2009 08:00:10 +0200 phylip (1:3.68-2) unstable; urgency=low * debian/control: Added myself to Uploaders. Vcs-* fields now point to trunk. * Simplified build process by removing 01_Makefile.patch and adjusting debian/rules. Removed commented out code from debian/rules. * Added a patch that prevents treedist from writing empty files on amd64. -- Manuel Prinz Sat, 01 Nov 2008 17:19:54 +0100 phylip (1:3.68-1) unstable; urgency=low * New upstream version -- Andreas Tille Sun, 17 Aug 2008 11:40:34 -0300 phylip (1:3.67-3) unstable; urgency=low [ Andreas Tille ] * Added XS-Autobuild: yes to enable auto building * Standards-Version: 3.8.0 (no changes needed) * debian/README.Debian: s?usr/doc?usr/share/doc? [ Charles Plessy ] * Changed the doc-base section according to the new policy. -- Andreas Tille Tue, 22 Jul 2008 15:51:33 +0200 phylip (1:3.67-2) unstable; urgency=low * Group maintenance: - Maintainer: Debian-Med Packaging Team - XS-DM-Upload-Allowed: Yes - Uploaders: Andreas Tille - Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phylip - Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/phylip * Standards-Version: 3.7.3 (no changes needed) * Homepage: http://evolution.genetics.washington.edu/phylip.html * Conversion of debian/copyright to UTF8 * Make use of quilt instead of simplepatchsys -- Andreas Tille Tue, 12 Feb 2008 18:29:32 +0100 phylip (1:3.67-1) unstable; urgency=low * New upstream version * Added watch file * No need for auto_update debian/control so removed this * phylip-doc package in section doc -- Andreas Tille Mon, 03 Sep 2007 09:47:35 +0200 phylip (1:3.66-1) unstable; urgency=low * New upstream version -- Andreas Tille Fri, 1 Sep 2006 23:30:58 +0200 phylip (1:3.65-1) unstable; urgency=low * New upstream version Closes: #367237 * Switched to cdbs * Debhelper 5 * Standards-Version: 3.7.2 * Fixed Copyright statement (Thanks to Charles Plessy) Closes: #381140 -- Andreas Tille Thu, 3 Aug 2006 21:17:58 +0200 phylip (1:3.6.1-2) unstable; urgency=low * Added Build-Depends: libx11-dev, libxt-dev, libxaw7-dev Thanks to Andreas Jochens Closes: #266650 -- Andreas Tille Wed, 18 Aug 2004 18:57:27 +0200 phylip (1:3.6.1-1) unstable; urgency=low * New upstream version * Moved from non-free/misc to section non-free/science * Switched to debhelper 4 * Standards-Version: 3.6.1 * Added doc-base * New version comes with extensive HTML documentation which was split up to separate Debian package -- Andreas Tille Tue, 13 Jul 2004 12:00:17 +0200 phylip (3.573c-7) unstable; urgency=low * Corrected spelling bug (Thanks to Matt Zimmerman ) closes: #125245 -- Andreas Tille Tue, 18 Dec 2001 11:56:36 +0100 phylip (3.573c-6) unstable; urgency=low * Forgot to close wnpp-bug so this upload closes: #100251 * Added URL to the package description because I consider this as "good style" to have an upstream link without installing the package * Added PhylipGuide document which can be found at http://www.es.embnet.org/~pprpc/activs/PHYLIPGuide/PhylipGuide-1.6.html -- Andreas Tille Tue, 30 Oct 2001 08:06:24 +0100 phylip (3.573c-5) unstable; urgency=low * New Maintainer * A patch by Patrice Godard fo fix #67657 is applied because it compiles well for me in contrast to 3.573c-2 where it was enclosed as patch.diff. closes: #67657 * Standards-Version: 3.5.6 -- Andreas Tille Tue, 23 Oct 2001 12:35:14 +0200 phylip (3.573c-4) unstable; urgency=low * Maintainer set to Debian QA Group . -- Adrian Bunk Fri, 24 Aug 2001 23:41:36 +0200 phylip (3.573c-3) unstable; urgency=low * Phylip manpage completely revised. -- Dr. Guenter Bechly Mon, 16 Apr 2001 19:21:10 +0200 phylip (3.573c-2) unstable; urgency=low * Package adopted by new maintainer; closes: #92789 * Moved manpage to /usr/share/man; closes: #91028 * Moved last file from /usr/doc to /usr/share/doc; closes: #91601 * Updated to latest policy, and added Build-Depends in control. * A patch by Patrice Godard fo fix #67657 is enclosed as patch.diff but was not applied since it failed to compile. -- Dr. Guenter Bechly Sat, 7 Apr 2001 16:00:14 +0200 phylip (3.573c-1) unstable; urgency=low * The wrapper displays the name of available programs. Closes #33382 * Switch to dh_make * New and better description. * New upstream release. Closes #36411. Patches in bug report #36475 does not seem to have been integrated upstream :-( So, I patched myself. Closes #36475. -- Stephane Bortzmeyer Tue, 18 May 1999 17:45:10 +0200 phylip (3.5c-3) unstable; urgency=low * Bug in dnapars fixed (incompatible with glibc). * New "tests" directory with samples. * Fonts now included (they were forgotten) -- Stephane Bortzmeyer Wed, 21 Oct 1998 17:01:02 +0200 phylip (3.5c-2) unstable; urgency=low * The many executables are replaced by a wrapper. First public release. -- Stephane Bortzmeyer Thu, 10 Sep 1998 10:43:11 +0200 phylip (3.5c-1) unstable; urgency=low * Initial Release. -- Stephane Bortzmeyer Fri, 28 Aug 1998 14:51:10 +0200 Local variables: mode: debian-changelog End: debian/phylip.10000644000000000000000000000224711110210221010537 0ustar .TH PHYLIP 1 "April 16, 2001" .SH NAME phylip \- runs various phylogenies programs .SH SYNOPSIS .B phylip .B program [arguments] .SH DESCRIPTION This manual page documents briefly the .B phylip wrapper to the Phylip programs. This manual page was written for the Debian GNU/Linux distribution because the original program did not have a manual page. .PP \fBphylip\fP is just a wrapper that invokes the various programs in the Phylip phylogeny software package. You can get more detailed documentation in /usr/share/doc/phylip where you find one helpfile for each program. .PP The following programs are included: clique, contrast, dnainvar, dnamove, dollop, drawgram, fitch, mix, penny, restml, consense, dnacomp, dnaml, dnapars, dolmove, drawtree, gendist, move, protdist, retree, contml, dnadist, dnamlk, dnapenny, dolpenny, factor, kitsch, neighbor, protpars, and seqboot. .SH OPTIONS There are no options. .SH EXAMPLES .IP phylip\ dnapenny .IP phylip\ factor .SH SEE ALSO .BR treetool (1), .br .SH AUTHOR This manual page was written by Stephane Bortzmeyer and Dr. Guenter Bechly , for the Debian GNU/Linux system (but may be used by others). debian/examples/0000755000000000000000000000000012200530436010777 5ustar debian/examples/treefile0000644000000000000000000000022411110210221012501 0ustar ((B.subtilis:0.78875,Brontosaur:0.00012):0.60550, (Hesperorni:0.22491,(B._virgini:0.00012,Baluchithe:0.18870):0.32474):0.13893, Archaeopt:0.44750); debian/examples/tests/0000755000000000000000000000000012200530436012141 5ustar debian/examples/tests/dna.data0000644000000000000000000000404611110210221013524 0ustar 7 232 Bovine CCAAACCTGT CCCCACCATC TAACACCAAC CCACATATAC AAGCTAAACC AAAAATACCA Mouse CCAAAAAAAC ATCCAAACAC CAACCCCAGC CCTTACGCAA TAGCCATACA AAGAATATTA Gibbon CTATACCCAC CCAACTCGAC CTACACCAAT CCCCACATAG CACACAGACC AACAACCTCC Orang CCCCACCCGT CTACACCAGC CAACACCAAC CCCCACCTAC TATACCAACC AATAACCTCT Gorilla CCCCATTTAT CCATAAAAAC CAACACCAAC CCCCATCTAA CACACAAACT AATGACCCCC Chimp CCCCATCCAC CCATACAAAC CAACATTACC CTCCATCCAA TATACAAACT AACAACCTCC Human CCCCACTCAC CCATACAAAC CAACACCACT CTCCACCTAA TATACAAATT AATAACCTCC TACTACTAAA AACTCAAATT AACTCTTTAA TCTTTATACA ACATTCCACC AACCTATCCA TACAACCATA AATAAGACTA ATCTATTAAA ATAACCCATT ACGATACAAA ATCCCTTTCG CACCTTCCAT ACCAAGCCCC GACTTTACCG CCAACGCACC TCATCAAAAC ATACCTACAA CAACCCCTAA ACCAAACACT ATCCCCAAAA CCAACACACT CTACCAAAAT ACACCCCCAA CACCCTCAAA GCCAAACACC AACCCTATAA TCAATACGCC TTATCAAAAC ACACCCCCAA CACTCTTCAG ACCGAACACC AATCTCACAA CCAACACGCC CCGTCAAAAC ACCCCTTCAG CACCTTCAGA ACTGAACGCC AATCTCATAA CCAACACACC CCATCAAAGC ACCCCTCCAA CACAAAAAAA CTCATATTTA TCTAAATACG AACTTCACAC AACCTTAACA CATAAACATA TCTAGATACA AACCACAACA CACAATTAAT ACACACCACA ATTACAATAC TAAACTCCCA CACAAACAAA TGCCCCCCCA CCCTCCTTCT TCAAGCCCAC TAGACCATCC TACCTTCCTA TTCACATCCG CACACCCCCA CCCCCCCTGC CCACGTCCAT CCCATCACCC TCTCCTCCCA CATAAACCCA CGCACCCCCA CCCCTTCCGC CCATGCTCAC CACATCATCT CTCCCCTTCA CACAAATTCA TACACCCCTA CCTTTCCTAC CCACGTTCAC CACATCATCC CCCCCTCTCA CACAAACCCG CACACCTCCA CCCCCCTCGT CTACGCTTAC CACGTCATCC CTCCCTCTCA CCCCAGCCCA ACACCCTTCC ACAAATCCTT AATATACGCA CCATAAATAA CA TCCCACCAAA TCACCCTCCA TCAAATCCAC AAATTACACA ACCATTAACC CA GCACGCCAAG CTCTCTACCA TCAAACGCAC AACTTACACA TACAGAACCA CA ACACCCTAAG CCACCTTCCT CAAAATCCAA AACCCACACA ACCGAAACAA CA ACACCTCAAT CCACCTCCCC CCAAATACAC AATTCACACA AACAATACCA CA ACATCTTGAC TCGCCTCTCT CCAAACACAC AATTCACGCA AACAACGCCA CA ACACCTTAAC TCACCTTCTC CCAAACGCAC AATTCGCACA CACAACGCCA CA debian/examples/tests/tree.data0000644000000000000000000000002211110210221013707 0ustar ((BM3,TERP),CAM); debian/examples/tests/Makefile0000644000000000000000000000151311110210221013563 0ustar # Makefile, tests directory and samples by Catherine Letondal test: testdna testprot testdist testtree testdna: rm -f infile ln -s dna.data infile make testprog PROGRAM=dnapars make testprog PROGRAM=dnaml make testprog PROGRAM=dnadist testprot: rm -f infile ln -s prot.data infile make testprog PROGRAM=protpars make testprog PROGRAM=protdist testdist: rm -f infile ln -s distance.data infile make testprog PROGRAM=neighbor testtree: rm -f intree ln -s tree.data intree echo 0 > params echo l >> params echo m >> params echo y >> params phylip drawtree < params > drawtree.out phylip drawgram < params > drawgram.out testprog: echo 0 > params echo y >> params phylip ${PROGRAM} < params > ${PROGRAM}.out rm -f outtree outfile clean: rm -f params infile *.out intree outfile outtree *~ debian/examples/tests/neighbor.version-3.5.x0000644000000000000000000000355711110210221016112 0ustar  Neighbor-Joining/UPGMA method version 3.5 Settings for this run: N Neighbor-joining or UPGMA tree? Neighbor-joining O Outgroup root? No, use as outgroup species 1 L Lower-triangular data matrix? No R Upper-triangular data matrix? No S Subreplicates? No J Randomize input order of species? No. Use input order M Analyze multiple data sets? No 0 Terminal type (IBM PC, VT52, ANSI)? ANSI 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Write out trees onto tree file? Yes Are these settings correct? (type Y or the letter for one to change) Neighbor-Joining/UPGMA method version 3.5 Settings for this run: N Neighbor-joining or UPGMA tree? Neighbor-joining O Outgroup root? No, use as outgroup species 1 L Lower-triangular data matrix? No R Upper-triangular data matrix? No S Subreplicates? No J Randomize input order of species? No. Use input order M Analyze multiple data sets? No 0 Terminal type (IBM PC, VT52, ANSI)? (none 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Write out trees onto tree file? Yes Are these settings correct? (type Y or the letter for one to change) CYCLE 4: OTU 1 ( 0.66204) JOINS OTU 2 ( 0.57646) CYCLE 3: OTU 6 ( 0.14924) JOINS OTU 7 ( 0.10776) CYCLE 2: OTU 5 ( 0.12276) JOINS NODE 6 ( 0.04809) CYCLE 1: NODE 1 ( 0.30172) JOINS OTU 3 ( 0.31418) LAST CYCLE: NODE 1 ( 0.03714) JOINS OTU 4 ( 0.21738) JOINS NODE 5 ( 0.03822) Output written on output file Tree written on tree file debian/examples/tests/dnapars.ok0000644000000000000000000000453511110210221014115 0ustar DNA parsimony algorithm, version 3.6b Setting for this run: U Search for best tree? Yes S Search option? More thorough search V Number of trees to save? 10000 J Randomize input order of sequences? No. Use input order O Outgroup root? No, use as outgroup species 1 T Use Threshold parsimony? No, use ordinary parsimony N Use Transversion parsimony? No, count all steps W Sites weighted? No M Analyze multiple data sets? No I Input sequences interleaved? Yes 0 Terminal type (IBM PC, ANSI, none)? (none) 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Print out steps in each site No 5 Print sequences at all nodes of tree No 6 Write out trees onto tree file? Yes Y to accept these or type the letter for one to change  DNA parsimony algorithm, version 3.6b Setting for this run: U Search for best tree? Yes S Search option? More thorough search V Number of trees to save? 10000 J Randomize input order of sequences? No. Use input order O Outgroup root? No, use as outgroup species 1 T Use Threshold parsimony? No, use ordinary parsimony N Use Transversion parsimony? No, count all steps W Sites weighted? No M Analyze multiple data sets? No I Input sequences interleaved? Yes 0 Terminal type (IBM PC, ANSI, none)? IBM PC 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Print out steps in each site No 5 Print sequences at all nodes of tree No 6 Write out trees onto tree file? Yes Y to accept these or type the letter for one to change Adding species: 1. Bovine 2. Mouse 3. Gibbon 4. Orang 5. Gorilla 6. Chimp 7. Human Doing global rearrangements on all trees tied for best !-------------! ............. ............. Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Done. debian/examples/tests/neighbor.ok0000644000000000000000000000357011110210221014260 0ustar Neighbor-Joining/UPGMA method version 3.6b Settings for this run: N Neighbor-joining or UPGMA tree? Neighbor-joining O Outgroup root? No, use as outgroup species 1 L Lower-triangular data matrix? No R Upper-triangular data matrix? No S Subreplicates? No J Randomize input order of species? No. Use input order M Analyze multiple data sets? No 0 Terminal type (IBM PC, ANSI, none)? (none) 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Write out trees onto tree file? Yes Y to accept these or type the letter for one to change  Neighbor-Joining/UPGMA method version 3.6b Settings for this run: N Neighbor-joining or UPGMA tree? Neighbor-joining O Outgroup root? No, use as outgroup species 1 L Lower-triangular data matrix? No R Upper-triangular data matrix? No S Subreplicates? No J Randomize input order of species? No. Use input order M Analyze multiple data sets? No 0 Terminal type (IBM PC, ANSI, none)? IBM PC 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Write out trees onto tree file? Yes Y to accept these or type the letter for one to change Cycle 4: species 1 ( 0.66204) joins species 2 ( 0.57646) Cycle 3: species 6 ( 0.14924) joins species 7 ( 0.10776) Cycle 2: species 5 ( 0.12276) joins node 6 ( 0.04809) Cycle 1: species 4 ( 0.21738) joins node 5 ( 0.03822) last cycle: node 1 ( 0.30172) joins species 3 ( 0.31418) joins node 4 ( 0.03714) Output written on file "outfile" Tree written on file "outtree" Done. debian/examples/tests/prot.data0000644000000000000000000000363211110210221013746 0ustar 3 474 CAM ---TTETIQS NANLAPLPPH VPEHLVFDFD MYNPSN--LS AGVQEAWAVL TERP ----MDARAT IPEHIARTVI LPQGYADDEV IYPAFK--WL RDEQPLAMAH BM3 TIKEMPQPKT FGELKNLPLL NTDKPVQALM KIADELGEIF KFEAPGRVTR QESNVPDLVW TRCNGG---H WIATRGQLIR EAY-EDYRHF SSECPFIPRE IEGYDPMWIA TKHADV---M QIGKQPGLFS NAEGSEILYD QNNEAFMRSI YLS-SQRLIK EACDESRFDK NLSQALKFVR DFAGDGLFTS WTHEKNWKKA AGEAYDFIP- -TSMDPPEQR QFRALANQVV GMPVVDKLEN RIQELACSLI SGGCPHVIDS LTSMDPPTHT AYRGLTLNWF QPASIRKLEE NIRRIAQASV HNILLPSFS- -QQAMKGYHA MMVDIAVQLV QKWERLNADE HIEVPEDMTR ESLR-PQGQC NFTEDYAEPF PIRIFMLLAG LPEEDIPHLK YLTDQMT--- QRLLDFDGEC DFMTDCALYY PLHVVMTALG VPEDDEPLML KLTQDFFGVH LTLD-TIGLC GFNYRFNSFY RDQPHPFITS MVRALDEAMN KLQRANP--D RPD------- ------GSMT FAEAKEALYD YLIPIIEQRR QKP--GTDAI EPDEQAVAAP RQSADEAARR FHETIATFYD YFNGFTVDRR SCP--KDDVM DPAYD----- -----ENKRQ FQEDIKVMND LVDKIIADRK ASGEQSDDLL SIVANGQVN- -GRPITSDEA KRMCGLLLVG GLDTVVNFLS FSMEFLAKSP SLLANSKLD- -GNYIDDKYI NAYYVAIATA GHDTTSSSSG GAIIGLSRNP THMLNGKDPE TGEPLDDENI RYQIITFLIA GHETTSGLLS FALYFLVKNP EHRQELIERP E--------- --------RI PAACEELLRR FS-LVADGRI EQLALAKSDP A--------- --------LI PRLVDEAVRW TAPVKSFMRT HVLQKAAEEA ARVLVDPVPS YKQVKQLKYV GMVLNEALRL WPTAPAFSLY LTSDYEFHGV Q-LKKGDQIL LPQMLSGLDE REN-ACPMHV DFSRQK---- ALADTEVRGQ N-IKRGDRIM LSYPSANRDE EVF-SNPDEF DITRFP---- AKEDTVLGGE YPLEKGDELM VLIPQLHRDK TIWGDDVEEF RPERFENPSA ---VSHTTFG HGSHLCLGQH LARREIIVTL KEWLTRIPDF SIAPGAQIQH ---NRHLGFG WGAHMCLGQH LAKLEMKIFF EELLPKLKSV ELS-GPPRLV IPQHAFKPFG NGQRACIGQQ FALHEATLVL GMMLKHFDFE DHT-NYELDI KSGIVSGVQA LPLVWDPATT KAV- ATNFVGGPKN VPIRFTKA-- ---- KETLTLKPEG FVVKAKSKKI PLGG debian/examples/tests/dnaml.ok0000644000000000000000000000441411110210221013554 0ustar Nucleic acid sequence Maximum Likelihood method, version 3.6b Settings for this run: U Search for best tree? Yes T Transition/transversion ratio: 2.0000 F Use empirical base frequencies? Yes C One category of sites? Yes R Rate variation among sites? constant rate W Sites weighted? No S Speedier but rougher analysis? Yes G Global rearrangements? No J Randomize input order of sequences? No. Use input order O Outgroup root? No, use as outgroup species 1 M Analyze multiple data sets? No I Input sequences interleaved? Yes 0 Terminal type (IBM PC, ANSI, none)? (none) 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Write out trees onto tree file? Yes 5 Reconstruct hypothetical sequences? No Y to accept these or type the letter for one to change Nucleic acid sequence Maximum Likelihood method, version 3.6b Settings for this run: U Search for best tree? Yes T Transition/transversion ratio: 2.0000 F Use empirical base frequencies? Yes C One category of sites? Yes R Rate variation among sites? constant rate W Sites weighted? No S Speedier but rougher analysis? Yes G Global rearrangements? No J Randomize input order of sequences? No. Use input order O Outgroup root? No, use as outgroup species 1 M Analyze multiple data sets? No I Input sequences interleaved? Yes 0 Terminal type (IBM PC, ANSI, none)? IBM PC 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Write out trees onto tree file? Yes 5 Reconstruct hypothetical sequences? No Y to accept these or type the letter for one to change Adding species: 1. Bovine 2. Mouse 3. Gibbon 4. Orang 5. Gorilla 6. Chimp 7. Human Output written to file "outfile" Tree also written onto file "outtree" Done. debian/examples/tests/distance.data0000644000000000000000000000073311110210221014553 0ustar 7 Bovine 0.0000 1.2385 1.3472 1.2070 1.0857 1.2832 1.2402 Mouse 1.2385 0.0000 1.1231 1.0966 1.1470 1.2157 1.1530 Gibbon 1.3472 1.1231 0.0000 0.5924 0.5077 0.5466 0.5001 Orang 1.2070 1.0966 0.5924 0.0000 0.3857 0.4405 0.4092 Gorilla 1.0857 1.1470 0.5077 0.3857 0.0000 0.3170 0.2817 Chimp 1.2832 1.2157 0.5466 0.4405 0.3170 0.0000 0.2570 Human 1.2402 1.1530 0.5001 0.4092 0.2817 0.2570 0.0000 debian/examples/infile0000644000000000000000000000045011110210221012151 0ustar 5 42 Turkey AAGCTNGGGC ATTTCAGGGT Salmo gairAAGCCTTGGC AGTGCAGGGT H. SapiensACCGGTTGGC CGTTCAGGGT Chimp AAACCCTTGC CGTTACGCTT Gorilla AAACCCTTGC CGGTACGCTT GAGCCCGGGC AATACAGGGT AT GAGCCGTGGC CGGGCACGGT AT ACAGGTTGGC CGTTCAGGGT AA AAACCGAGGC CGGGACACTC AT AAACCATTGC CGGTACGCTT AA debian/examples/README0000644000000000000000000000013111110210221011634 0ustar The 'infile' file contains DNA and is suitable for DNA-analysis programs like dnapenny. debian/compat0000644000000000000000000000000212200526127010361 0ustar 9 debian/control0000644000000000000000000000350312200732171010565 0ustar Source: phylip Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Manuel Prinz Section: non-free/science Priority: optional Build-Depends: debhelper (>= 9), libx11-dev, libxt-dev, libxaw7-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/phylip/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/phylip/trunk/ Homepage: http://evolution.genetics.washington.edu/phylip.html XS-Autobuild: yes Package: phylip Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: phylip-doc Description: package of programs for inferring phylogenies The PHYLogeny Inference Package is a package of programs for inferring phylogenies (evolutionary trees) from sequences. 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, distance matrices, and 0/1 discrete characters. Package: phylip-doc Architecture: all Section: non-free/doc Depends: ${misc:Depends} Suggests: phylip Description: package of programs for inferring phylogenies (documentation) The PHYLogeny Inference Package is a package of programs for inferring phylogenies (evolutionary trees) from sequences. 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, distance matrices, and 0/1 discrete characters. . This package contains the HTML documentation