[med-svn] r1209 - in trunk/packages: . phylip phylip/trunk phylip/trunk/debian phylip/trunk/debian/bin phylip/trunk/debian/examples phylip/trunk/debian/examples/tests phylip/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Mon Jan 28 15:49:40 UTC 2008
Author: tille
Date: 2008-01-28 15:49:40 +0000 (Mon, 28 Jan 2008)
New Revision: 1209
Added:
trunk/packages/phylip/
trunk/packages/phylip/trunk/
trunk/packages/phylip/trunk/debian/
trunk/packages/phylip/trunk/debian/README.debian
trunk/packages/phylip/trunk/debian/bin/
trunk/packages/phylip/trunk/debian/bin/phylip
trunk/packages/phylip/trunk/debian/changelog
trunk/packages/phylip/trunk/debian/compat
trunk/packages/phylip/trunk/debian/control
trunk/packages/phylip/trunk/debian/copyright
trunk/packages/phylip/trunk/debian/examples/
trunk/packages/phylip/trunk/debian/examples/README
trunk/packages/phylip/trunk/debian/examples/infile
trunk/packages/phylip/trunk/debian/examples/tests/
trunk/packages/phylip/trunk/debian/examples/tests/Makefile
trunk/packages/phylip/trunk/debian/examples/tests/distance.data
trunk/packages/phylip/trunk/debian/examples/tests/dna.data
trunk/packages/phylip/trunk/debian/examples/tests/dnaml.ok
trunk/packages/phylip/trunk/debian/examples/tests/dnapars.ok
trunk/packages/phylip/trunk/debian/examples/tests/neighbor.ok
trunk/packages/phylip/trunk/debian/examples/tests/neighbor.version-3.5.x
trunk/packages/phylip/trunk/debian/examples/tests/prot.data
trunk/packages/phylip/trunk/debian/examples/tests/tree.data
trunk/packages/phylip/trunk/debian/examples/treefile
trunk/packages/phylip/trunk/debian/patches/
trunk/packages/phylip/trunk/debian/patches/Makefile.diff
trunk/packages/phylip/trunk/debian/patches/src_Makefile.diff
trunk/packages/phylip/trunk/debian/patches/src_phylip_h.diff
trunk/packages/phylip/trunk/debian/phylip-doc.doc-base
trunk/packages/phylip/trunk/debian/phylip-doc.install
trunk/packages/phylip/trunk/debian/phylip-doc.links
trunk/packages/phylip/trunk/debian/phylip.1
trunk/packages/phylip/trunk/debian/phylip.examples
trunk/packages/phylip/trunk/debian/phylip.install
trunk/packages/phylip/trunk/debian/phylip.manpages
trunk/packages/phylip/trunk/debian/rules
trunk/packages/phylip/trunk/debian/watch
Log:
Added phylip.
Added: trunk/packages/phylip/trunk/debian/README.debian
===================================================================
--- trunk/packages/phylip/trunk/debian/README.debian (rev 0)
+++ trunk/packages/phylip/trunk/debian/README.debian 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,29 @@
+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/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 <gbechly at debian.org>, Sat, 7 Apr 2001 16:00:14 +0200
+
+The current Debian Maintainer is:
+ Andreas Tille <tille at debian.org> Tue, 23 Oct 2001 12:35:14 +0200
+
\ No newline at end of file
Added: trunk/packages/phylip/trunk/debian/bin/phylip
===================================================================
--- trunk/packages/phylip/trunk/debian/bin/phylip (rev 0)
+++ trunk/packages/phylip/trunk/debian/bin/phylip 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,24 @@
+#!/bin/sh
+
+BINDIR=/usr/lib/phylip/bin
+
+if [ $# -lt 1 ] ; then
+ echo "Usage: $0 <program>" 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
Added: trunk/packages/phylip/trunk/debian/changelog
===================================================================
--- trunk/packages/phylip/trunk/debian/changelog (rev 0)
+++ trunk/packages/phylip/trunk/debian/changelog 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,148 @@
+phylip (1:3.67-2) unstable; urgency=low
+
+ * Group maintenance:
+ - Maintainer: Debian-Med Packaging Team
+ <debian-med-packaging at lists.alioth.debian.org>
+ - XS-DM-Upload-Allowed: Yes
+ - Uploaders: Andreas Tille <tille at debian.org>
+ - 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
+
+ -- Andreas Tille <tille at debian.org> Mon, 28 Jan 2008 07:38:51 +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 <tille at debian.org> Mon, 03 Sep 2007 09:47:35 +0200
+
+phylip (1:3.66-1) unstable; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> 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 <aj at andaco.de>
+ Closes: #266650
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> Tue, 13 Jul 2004 12:00:17 +0200
+
+phylip (3.573c-7) unstable; urgency=low
+
+ * Corrected spelling bug (Thanks to Matt Zimmerman <mdz at debian.org>)
+ closes: #125245
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> Tue, 30 Oct 2001 08:06:24 +0100
+
+phylip (3.573c-5) unstable; urgency=low
+
+ * New Maintainer
+ * A patch by Patrice Godard <pgodard at pasteur.fr> 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 <tille at debian.org> Tue, 23 Oct 2001 12:35:14 +0200
+
+phylip (3.573c-4) unstable; urgency=low
+
+ * Maintainer set to Debian QA Group <packages at qa.debian.org>.
+
+ -- Adrian Bunk <bunk at fs.tum.de> Fri, 24 Aug 2001 23:41:36 +0200
+
+phylip (3.573c-3) unstable; urgency=low
+
+ * Phylip manpage completely revised.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> 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 <pgodard at pasteur.fr> fo fix #67657 is enclosed as
+ patch.diff but was not applied since it failed to compile.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> 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 <bortzmeyer at debian.org> 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 <bortzmeyer at debian.org> 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 <bortzmeyer at debian.org> Thu, 10 Sep 1998 10:43:11 +0200
+
+phylip (3.5c-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Stephane Bortzmeyer <bortzmeyer at pasteur.fr> Fri, 28 Aug 1998 14:51:10 +0200
+
+Local variables:
+mode: debian-changelog
+End:
Added: trunk/packages/phylip/trunk/debian/compat
===================================================================
--- trunk/packages/phylip/trunk/debian/compat (rev 0)
+++ trunk/packages/phylip/trunk/debian/compat 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1 @@
+5
Added: trunk/packages/phylip/trunk/debian/control
===================================================================
--- trunk/packages/phylip/trunk/debian/control (rev 0)
+++ trunk/packages/phylip/trunk/debian/control 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,40 @@
+Source: phylip
+Section: non-free/science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+XS-DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25), debhelper (>= 5), libx11-dev, libxt-dev, libxaw7-dev
+Standards-Version: 3.7.3
+Homepage: http://evolution.genetics.washington.edu/phylip.html
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phylip
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/phylip
+
+Package: phylip
+Section: non-free/science
+Architecture: any
+Depends: ${shlibs:Depends}
+Suggests: phylip-doc
+Description: [Biology] A 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
+Section: non-free/doc
+Architecture: all
+Suggests: phylip
+Description: [Biology] A 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.
+ .
+ This package contains the HTML documentation
Added: trunk/packages/phylip/trunk/debian/copyright
===================================================================
--- trunk/packages/phylip/trunk/debian/copyright (rev 0)
+++ trunk/packages/phylip/trunk/debian/copyright 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,35 @@
+This package was debianized by Andreas Tille <tille at debian.org> 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 <joe at genetics.washington.edu>
+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 .
Added: trunk/packages/phylip/trunk/debian/examples/README
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/README (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/README 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,3 @@
+The 'infile' file contains DNA and is suitable for DNA-analysis
+programs like dnapenny.
+
Added: trunk/packages/phylip/trunk/debian/examples/infile
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/infile (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/infile 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,12 @@
+ 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
Added: trunk/packages/phylip/trunk/debian/examples/tests/Makefile
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/tests/Makefile (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/tests/Makefile 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,42 @@
+# Makefile, tests directory and samples by Catherine Letondal <letondal at pasteur.fr>
+
+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 *~
+
Added: trunk/packages/phylip/trunk/debian/examples/tests/distance.data
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/tests/distance.data (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/tests/distance.data 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,8 @@
+ 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
Added: trunk/packages/phylip/trunk/debian/examples/tests/dna.data
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/tests/dna.data (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/tests/dna.data 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,32 @@
+ 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
Added: trunk/packages/phylip/trunk/debian/examples/tests/dnaml.ok
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/tests/dnaml.ok (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/tests/dnaml.ok 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,66 @@
+
+
+
+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
+[2J[HNucleic 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.
+
Added: trunk/packages/phylip/trunk/debian/examples/tests/dnapars.ok
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/tests/dnapars.ok (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/tests/dnapars.ok 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,71 @@
+
+
+
+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
+[2J[H
+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.
+
Added: trunk/packages/phylip/trunk/debian/examples/tests/neighbor.ok
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/tests/neighbor.ok (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/tests/neighbor.ok 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,55 @@
+
+
+
+
+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
+[2J[H
+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.
+
Added: trunk/packages/phylip/trunk/debian/examples/tests/neighbor.version-3.5.x
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/tests/neighbor.version-3.5.x (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/tests/neighbor.version-3.5.x 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,50 @@
+
+[2J[H
+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
+
Added: trunk/packages/phylip/trunk/debian/examples/tests/prot.data
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/tests/prot.data (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/tests/prot.data 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,40 @@
+ 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
Added: trunk/packages/phylip/trunk/debian/examples/tests/tree.data
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/tests/tree.data (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/tests/tree.data 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1 @@
+((BM3,TERP),CAM);
Added: trunk/packages/phylip/trunk/debian/examples/treefile
===================================================================
--- trunk/packages/phylip/trunk/debian/examples/treefile (rev 0)
+++ trunk/packages/phylip/trunk/debian/examples/treefile 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,3 @@
+((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);
Added: trunk/packages/phylip/trunk/debian/patches/Makefile.diff
===================================================================
--- trunk/packages/phylip/trunk/debian/patches/Makefile.diff (rev 0)
+++ trunk/packages/phylip/trunk/debian/patches/Makefile.diff 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,28 @@
+--- Makefile.orig 2006-08-04 08:39:03.000000000 +0200
++++ Makefile 2006-08-04 08:52:32.000000000 +0200
+@@ -0,0 +1,25 @@
++# Wrapper Makefile to simplify use of cdbs
++# Copyright: Andreas Tille <tille at debian.org>; GPL
++
++all:
++ cd src; make all
++
++install:
++ cd src; make install CFLAGS="-g -O3 -fomit-frame-pointer" DATADIR=../fonts
++
++put:
++ cd src; make put
++
++clean:
++ cd src; make clean
++
++# Does not help for cdbs because patches are reverted before calling dh_clean
++# So exe/* is removed in debian/rules
++#distclean:
++# make clean
++# rm -f exe/*
++
++test:
++
++dnaml:
++ cd src; make dnaml
Added: trunk/packages/phylip/trunk/debian/patches/src_Makefile.diff
===================================================================
--- trunk/packages/phylip/trunk/debian/patches/src_Makefile.diff (rev 0)
+++ trunk/packages/phylip/trunk/debian/patches/src_Makefile.diff 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,37 @@
+--- src/Makefile.orig 2007-07-24 00:12:22.000000000 +0200
++++ src/Makefile 2007-09-03 09:59:23.000000000 +0200
+@@ -45,6 +45,7 @@
+ #
+ # the following specifies the directory where the executables will be placed
+ EXEDIR = ../exe
++DATADIR = ../exe
+ #
+ # ----------------------------------------------------------------------------
+ #
+@@ -189,8 +190,10 @@
+ @echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
+ @mkdir -p $(EXEDIR)
+ @cp $(PROGS) $(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 "Finished installation."
+ @echo ""
+
+@@ -207,6 +210,13 @@
+ @echo "Finished cleanup."
+ @echo ""
+
++distclean:
++ @make 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)
Added: trunk/packages/phylip/trunk/debian/patches/src_phylip_h.diff
===================================================================
--- trunk/packages/phylip/trunk/debian/patches/src_phylip_h.diff (rev 0)
+++ trunk/packages/phylip/trunk/debian/patches/src_phylip_h.diff 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,11 @@
+--- src/phylip.h.orig 2005-08-25 23:48:38.000000000 +0200
++++ src/phylip.h 2006-08-05 23:00:22.000000000 +0200
+@@ -64,7 +64,7 @@
+ #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"
Added: trunk/packages/phylip/trunk/debian/phylip-doc.doc-base
===================================================================
--- trunk/packages/phylip/trunk/debian/phylip-doc.doc-base (rev 0)
+++ trunk/packages/phylip/trunk/debian/phylip-doc.doc-base 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,16 @@
+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: Apps/Science
+
+Format: html
+Index: /usr/share/doc/phylip/html/index.html
+Files: /usr/share/doc/phylip/html/*
Added: trunk/packages/phylip/trunk/debian/phylip-doc.install
===================================================================
--- trunk/packages/phylip/trunk/debian/phylip-doc.install (rev 0)
+++ trunk/packages/phylip/trunk/debian/phylip-doc.install 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,2 @@
+doc usr/share/doc/phylip/html
+phylip.* usr/share/doc/phylip/html
Added: trunk/packages/phylip/trunk/debian/phylip-doc.links
===================================================================
--- trunk/packages/phylip/trunk/debian/phylip-doc.links (rev 0)
+++ trunk/packages/phylip/trunk/debian/phylip-doc.links 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,2 @@
+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
Added: trunk/packages/phylip/trunk/debian/phylip.1
===================================================================
--- trunk/packages/phylip/trunk/debian/phylip.1 (rev 0)
+++ trunk/packages/phylip/trunk/debian/phylip.1 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,34 @@
+.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 <bortzmeyer at debian.org>
+and Dr. Guenter Bechly <gbechly at debian.org>, for the Debian GNU/Linux system
+(but may be used by others).
Added: trunk/packages/phylip/trunk/debian/phylip.examples
===================================================================
--- trunk/packages/phylip/trunk/debian/phylip.examples (rev 0)
+++ trunk/packages/phylip/trunk/debian/phylip.examples 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1 @@
+debian/examples/*
Added: trunk/packages/phylip/trunk/debian/phylip.install
===================================================================
--- trunk/packages/phylip/trunk/debian/phylip.install (rev 0)
+++ trunk/packages/phylip/trunk/debian/phylip.install 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,3 @@
+exe/* usr/lib/phylip/bin
+fonts/* usr/share/phylip/
+debian/bin/phylip usr/bin
Added: trunk/packages/phylip/trunk/debian/phylip.manpages
===================================================================
--- trunk/packages/phylip/trunk/debian/phylip.manpages (rev 0)
+++ trunk/packages/phylip/trunk/debian/phylip.manpages 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1 @@
+debian/phylip.1
Added: trunk/packages/phylip/trunk/debian/rules
===================================================================
--- trunk/packages/phylip/trunk/debian/rules (rev 0)
+++ trunk/packages/phylip/trunk/debian/rules 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,17 @@
+#!/usr/bin/make -f
+# debian/rules for phylip using cdbs
+# Andreas Tille <tille at debian.org>, GPL
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/perlmodule.mk
+
+# dh_clean expects a Makefile which was just removed by redoing the patches ...
+# This hack circumvents the problem
+clean::
+ rm -fr exe/* fonts
+
+# cd src; $(MAKE) install CFLAGS="-g -O3 -fomit-frame-pointer" DATADIR=../fonts
+# cd src; $(MAKE) distclean DATADIR=../fonts
+# dh_install -i --exclude $(pkg).html
+# sed 's?"doc/?"html/?g' doc/$(pkg).html > debian/$(pkg)/usr/share/doc/$(pkg)/$(pkg).html
Property changes on: trunk/packages/phylip/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/phylip/trunk/debian/watch
===================================================================
--- trunk/packages/phylip/trunk/debian/watch (rev 0)
+++ trunk/packages/phylip/trunk/debian/watch 2008-01-28 15:49:40 UTC (rev 1209)
@@ -0,0 +1,9 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+http://evolution.gs.washington.edu/phylip/download/phylip-(.*)\.tar\.gz
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