debian/0000755000000000000000000000000011735046025007171 5ustar debian/upstream0000644000000000000000000000100711735045644010760 0ustar Homepage: http://tree.bio.ed.ac.uk/software/seqgen/ Name: Seq-Gen Reference: Author: Rambaut, A. and Grassly, N. C. Title: "Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees" Journal: Comput. Appl. Biosci. Volume: 13 Number: 3 Pages: 235-238 Year: 1997 PMID: 9183526 DOI: 10.1093/bioinformatics/13.3.235 URL: http://bioinformatics.oxfordjournals.org/content/13/3/235.abstract eprint: http://bioinformatics.oxfordjournals.org/content/13/3/235.full.pdf debian/source/0000755000000000000000000000000011735043420010465 5ustar debian/source/format0000644000000000000000000000001411535150473011700 0ustar 3.0 (quilt) debian/seq-gen.install0000644000000000000000000000003211536737132012120 0ustar source/seq-gen /usr/bin/ debian/seq-gen.docs0000644000000000000000000000011011536737155011404 0ustar documentation/Seq-Gen.Manual.html documentation/Using_Seq-Gen_with_PAUP debian/seq-gen.10000644000000000000000000000502711735043366010623 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH SEQ-GEN "1" "March 2011" "seq-gen 1.3.3" "User Commands" .SH NAME seq-gen \- Sequence Generator .SH SYNOPSIS .B seq-gen [\fI-m MODEL\fR] [\fI-l #\fR] [\fI-n #\fR] [\fI-p #\fR] [\fI-s # | \-d #\fR] [\fI-k #\fR][\-c #1 #2 #3 | \-a\fR # [\-g #]] [\-f e | #] [\-t # | \-r\fR #][\-z #] [\-o[p][r][n]] [\-w[a][r]] [\-x NAME] [\-q] [\-h] [treefile] .SH DESCRIPTION Sequence Generator \- seq\-gen Version 1.3.3 .IP .HP \fB\-l\fR: # = sequence length [default = 1000]. .HP \fB\-n\fR: # = simulated datasets per tree [default = 1]. .HP \fB\-p\fR: # = number of partitions (and trees) per sequence [default = 1]. .HP \fB\-s\fR: # = branch length scaling factor [default = 1.0]. .HP \fB\-d\fR: # = total tree scale [default = use branch lengths]. .HP \fB\-k\fR: # = use sequence k as ancestral (needs alignment) [default = random]. .IP Substitution model options: .HP \fB\-m\fR: MODEL = HKY, F84, GTR, JTT, WAG, PAM, BLOSUM, MTREV, GENERAL .IP HKY, F84 & GTR are for nucleotides the rest are for amino acids .HP \fB\-a\fR: # = shape (alpha) for gamma rate heterogeneity [default = none]. .HP \fB\-g\fR: # = number of gamma rate categories [default = continuous]. .HP \fB\-i\fR: # = proportion of invariable sites [default = 0.0]. .IP Nucleotid model specific options: .HP \fB\-c\fR: #1 #2 #3 = rates for codon position heterogeneity [default = none]. .HP \fB\-t\fR: # = transition\-transversion ratio [default = equal rate]. .HP \fB\-r\fR: #1 #2 #3 #4 #5 #6= general rate matrix [default = all 1.0]. .HP \fB\-f\fR: #A #C #G #T = nucleotide frequencies [default = all equal]. .IP Amino Acid model specific options: .IP specify using the order ARNDCQEGHILKMFPSTWYV .HP \fB\-r\fR: #1 .. #190 = general rate matrix [default = all 1.0]. .HP \fB\-f\fR: #1 .. #20 = amino acid frequencies e=equal [default = matrix freqs]. .IP Miscellaneous options: .HP \fB\-z\fR: # = seed for random number generator [default = system generated]. .HP \fB\-o\fR: Output file format [default = PHYLIP] .IP p PHYLIP format r relaxed PHYLIP format n NEXUS format .HP \fB\-w\fR: Write additional information [default = none] .IP a Write ancestral sequences for each node r Write rate for each site .HP \fB\-x\fR: NAME = a text file to insert after every dataset [default = none]. .HP \fB\-h\fR: Give this help message .HP \fB\-q\fR: Quiet .IP treefile: name of tree file [default = trees on stdin] .SH AUTHOR (c) Copyright, 1996\-2004 Andrew Rambaut and Nick Grassly Department of Zoology, University of Oxford South Parks Road, Oxford OX1 3PS, U.K. debian/seq-gen.examples0000644000000000000000000000001311535150473012263 0ustar examples/* debian/copyright0000644000000000000000000000546011735043366011136 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: seq-gen Source: http://tree.bio.ed.ac.uk/software/seqgen/ Files: * Copyright: © Copyright (c)1996-2011, Andrew Rambaut & Nick Grassly Institute of Evolutionary Biology, University of Edinburgh All rights reserved. License: BSD Files: source/eigen.* Copyright: © Copyright (c)1993-2008, Ziheng Yang License: PAML Files: source/gamma.* Copyright: © Copyright (c)1993-2008, Ziheng Yang License: PAML Files: source/twister.c Copyright: © Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura, All rights reserved. License: BSD Files: debian/* Copyright: 2011 Alex Mestiashvili License: BSD Like seq-gen itself License: PAML The software package is provided "as is" without warranty of any kind. In no event shall the author or his employer be held responsible for any damage resulting from the use of this software, including but not limited to the frustration that you may experience in using the package. The program package, including source codes, example data sets, executables, and this documentation, is distributed free of charge for academic use only. Permission is granted to copy and use programs in the package provided no fee is charged for it and provided that this copyright notice is not removed. License: BSD Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3. The names of its contributors may not be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. debian/compat0000644000000000000000000000000211735045753010376 0ustar 9 debian/get-orig-source0000755000000000000000000000240211735043366012135 0ustar #!/bin/bash #one should run uscan --force-download in order to run get-orig-source. #taken from figtree get-orig-source PKG=`dpkg-parsechangelog | awk '/Source:/ {print $2}'` if ! echo $@ | grep -q upstream-version ; then VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` else VERSION=`echo $@ | sed 's?^.*--upstream-version \([0-9.]\+\) .*download.html.*?\1?'` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi mkdir -p ../tarballs DLOADID=`grep "click here to start the downloa" ../download.html | awk -F'");print array[1]}'` SITE=`awk -F"\/" '/http/{print $1"/"$2"/"$3"/"}' debian/watch` wget $SITE/$DLOADID -O ../tarballs/${PKG}_${VERSION}.tgz rm -f ../download.html mkdir ../tarballs/${PKG}-${VERSION} #convert to proper name tar -xvf ../tarballs/${PKG}_${VERSION}.tgz -C ../tarballs/${PKG}-${VERSION}/ --strip-components=1 cd ../tarballs find ${PKG}-${VERSION}/ -type f -name "._*" -exec rm -f '{}' \; GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "$PKG"-"$VERSION" rm -rf "$PKG"-"$VERSION" rm -f "$PKG"_"$VERSION.tgz" echo "${PKG}_${VERSION}.orig.tar.gz is located in ../tarballs" debian/control0000644000000000000000000000263711735045761010612 0ustar Source: seq-gen Section: non-free/science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Alexandre Mestiashvili , Andreas Tille Build-Depends: debhelper (>= 9) Standards-Version: 3.9.3 Homepage: http://tree.bio.ed.ac.uk/software/seqgen/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seq-gen/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/seq-gen/trunk/ Package: seq-gen Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: simulate the evolution of nucleotide or amino acid sequences Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution. debian/seq-gen.doc-base0000644000000000000000000000052211536736670012141 0ustar Document: seq-gen Title: Manual for seq-gen Author: Andrew Rambaut1 and Nicholas C. Grass Abstract: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Section: Science/Biology Format: html Index: /usr/share/doc/seq-gen/Seq-Gen.Manual.html Files: /usr/share/doc/seq-gen/Seq-Gen.Manual.html debian/seq-gen.manpages0000644000000000000000000000001311535354615012244 0ustar debian/*.1 debian/watch0000644000000000000000000000021211675070021010211 0ustar version=3 http://tree.bio.ed.ac.uk/software/seqgen \ /download\.html\?name=seqgen&version=v(.*)&id=.* \ debian debian/get-orig-source debian/changelog0000644000000000000000000000202611735046025011043 0ustar seq-gen (1.3.3-1) unstable; urgency=low [ Alexandre Mestiashvili ] * New upstream release 1.3.3 * debian/control section changed to non-free/science * fixed debian/watch and debian/get-orig-source scripts * debian/seq-gen.1 fixed hyphen-used-as-minus-sign warning [ Andreas Tille ] * debian/control: Fixed Vcs fields * debian/upstream: Added citations * debhelper level 9 (control+compat) -- Andreas Tille Thu, 29 Mar 2012 13:30:11 +0200 seq-gen (1.3.2-2) unstable; urgency=low [ Alexandre Mestiashvili ] * fixed syntax-error-in-dep5-copyright warning [ Andreas Tille ] * Standards-Version: 3.9.2 (no changes needed) * debian/copyright: - License paragraph for packaging - License ist actually BSD license * Debhelper 8 (control+compat) -- Andreas Tille Thu, 27 Oct 2011 22:47:16 +0200 seq-gen (1.3.2-1) unstable; urgency=low * Initial release (Closes: #617340) -- Alexandre Mestiashvili Thu, 03 Mar 2011 14:58:34 +0000 debian/rules0000755000000000000000000000073011535426546010261 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 # This has to be exported to make some magic below work. export DH_OPTIONS %: dh $@ --sourcedirectory=source override_dh_clean: [ ! -f source/seq-gen ] || rm source/seq-gen dh_clean override_dh_installchangelogs: dh_installchangelogs documentation/Version_History override_dh_fixperms: dh_fixperms chmod 644 debian/seq-gen/usr/share/doc/seq-gen/examples/*