debian/0000755000000000000000000000000012244066113007165 5ustar debian/watch0000644000000000000000000000021412214301051010201 0ustar version=3 http://www.aevol.fr/download/index.php http://gforge.liris.cnrs.fr/frs/download.php/.*/aevol-(.*)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip) debian/copyright0000644000000000000000000000446612243764031011135 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: aevol Source: http://aevol.fr/download/ Files: * Copyright: 2003 - 2013 Guillaume Beslon 2003 - 2013 Carole Knibbe 2008 - 2013 David P. Parsons 2003 - 2007 Virginie Mathivet 2009 - 2013 Dusan Misevic 2010 - 2013 Antoine Frénoy 2011 - 2013 Bérénice Batut 2006 - 2009 Yolanda Sanchez-Dehesa 2010 - 2010 Guillaume Debras 2011 - 2011 Renaud Dessales 2010 - 2013 Stephan Fischer 2009 - 2009 Yann Hourdel 2013 - 2013 Charles Rocabert 2009 - 2009 Elie Rotenberg 2011 - 2011 Florian Thoni License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". Files: debian/* Copyright: 2013 David Parsons License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". debian/changelog0000644000000000000000000000023012243764031011035 0ustar aevol (4.2-1) unstable; urgency=low * Initial release (Closes: #718887) -- David Parsons Fri, 22 Nov 2013 16:10:43 +0100 debian/aevol_run.10000644000000000000000000000224112243764031011243 0ustar .TH AEVOL "1" "August 2013" "aevol 4.2" "User Manual" .SH NAME aevol \- an in silico experimental evolution platform .SH SYNOPSIS .B aevol_run_X11 \-h | .B \-\-help .br .B aevol_run_X11 \-V | .B \-\-version .br .B aevol_run_X11 \fR[\fB\-r\fI GENERATION\fR] \fR[\fB\-n\fI NB_GENER\fR] \fR[\fB\-tvwx\fR] .SH DESCRIPTION .B Aevol is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome. .TP .B aevol_run, aevol_run_X11 run an aevol simulation. .SH OPTIONS .TP .B \-h, \-\-help print this help, then exit .TP .B \-V, \-\-version print version number, then exit .HP .B \-n, \-\-nbgener .I NB_GENER .br number of generations to be run .HP .B \-r, \-\-resume .I GENERATION .br resume simulation at given generation .TP .B \-t, \-\-text use text files instead of binary files when possible .TP .B \-v, \-\-verbose be verbose .TP .B \-w, \-\-wait pause after loading .TP .B \-x, \-\-noX don't display X outputs upon start .br send SIGUSR1 to switch X output on/off .SH "SEE ALSO" .B aevol_create, aevol_modify, aevol_propagate debian/aevol_run_X11.10000777000000000000000000000000012244066001013737 2aevol_run.1ustar debian/aevol_propagate.10000644000000000000000000000205012243764031012417 0ustar .TH AEVOL "1" "August 2013" "aevol 4.2" "User Manual" .SH NAME aevol \- an in silico experimental evolution platform .SH SYNOPSIS .B aevol_propagate \-h or .B \-\-help .br .B aevol_propagate \-V or .B \-\-version .br .B aevol_propagate \fR[\fB\-g\fI GENERATION\fR] \fR[\fB\-i\fI in_dir\fR] \fR[\fB\-o\fI out_dir\fR] \fR[\fB\-v\fR] .SH DESCRIPTION .B Aevol is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome. .TP .B aevol_propagate create a fresh copy of the experiment .SH OPTIONS .TP .B \-h, \-\-help print this help, then exit .TP .B \-V, \-\-version print version number, then exit .HP .B \-g, \-\-gener .I GENERATION .br specify generation number .HP .B \-i, \-\-in .I in_dir .br specify input directory (default ".") .HP .B \-o, \-\-out .I in_dir .br specify output directory (default "./output") .TP .B \-v, \-\-verbose be verbose .SH "SEE ALSO" .B aevol_create, aevol_run, aevol_modify debian/source/0000755000000000000000000000000012214301051010453 5ustar debian/source/format0000644000000000000000000000001412214301051011661 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000212214301051010351 0ustar 9 debian/aevol_create.10000644000000000000000000000147712243764031011714 0ustar .TH AEVOL "1" "August 2013" "aevol 4.2" "User Manual" .SH NAME aevol \- an in silico experimental evolution platform .SH SYNOPSIS .B aevol_create \-h or .B \-\-help .br .B aevol_create \-V or .B \-\-version .br .B aevol_create [\-f .I param_file] .SH DESCRIPTION .B Aevol is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome. .TP .B aevol_create create an experiment with setup as specified in .I param_file .SH OPTIONS .TP .B \-h, \-\-help print this help, then exit .TP .B \-V, \-\-version print version number, then exit .TP .B \-f, \-\-file .I param_file specify parameter file (default: param.in) .SH "SEE ALSO" .B aevol_run, aevol_modify, aevol_propagate debian/aevol_modify.10000644000000000000000000000164012243764031011730 0ustar .TH AEVOL "1" "August 2013" "aevol 4.2" "User Manual" .SH NAME aevol \- an in silico experimental evolution platform .SH SYNOPSIS .B aevol_modify \-h or .B \-\-help .br .B aevol_modify \-V or .B \-\-version .br .B aevol_modify \fR[\fB\-g\fI GENERATION\fR] \fR[\fB\-f\fI param_file\fR] .SH DESCRIPTION .B Aevol is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome. .TP .B aevol_modify modify an experiment as specified in .I param_file .SH OPTIONS .TP .B \-h, \-\-help print this help, then exit .TP .B \-V, \-\-version print version number, then exit .HP .B \-g, \-\-gener .I GENERATION .br specify generation number .HP .B \-f, \-\-file .I param_file .br specify parameter file (default: param.in) .SH "SEE ALSO" .B aevol_create, aevol_run, aevol_propagate debian/rules0000755000000000000000000000020712243764031010247 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ --with autotools-dev debian/aevol.manpages0000644000000000000000000000015712214301051012001 0ustar debian/aevol_create.1 debian/aevol_run.1 debian/aevol_run_X11.1 debian/aevol_modify.1 debian/aevol_propagate.1 debian/control0000644000000000000000000000304312243764031010573 0ustar Source: aevol Maintainer: Debian Med Packaging Team Uploaders: David Parsons Section: science Priority: optional Build-Depends: debhelper (>= 9.0), zlib1g-dev, autotools-dev, libx11-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/aevol/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/aevol/trunk/ Homepage: http://www.aevol.fr/ Package: aevol Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: digital genetics model to run Evolution Experiments in silico Aevol is a digital genetics model: populations of digital organisms are subjected to a process of selection and variation, which creates a Darwinian dynamics. . By modifying the characteristics of selection (e.g. population size, type of environment, environmental variations) or variation (e.g. mutation rates, chromosomal rearrangement rates, types of rearrangements, horizontal transfer), one can study experimentally the impact of these parameters on the structure of the evolved organisms. In particular, since Aevol integrates a precise and realistic model of the genome, it allows for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences). . The simulation platform comes along with a set of tools for analysing phylogenies and measuring many characteristics of the organisms and populations along evolution. debian/docs0000644000000000000000000000001412214301051010021 0ustar NEWS README debian/upstream0000644000000000000000000000370312243753246010764 0ustar Reference: - Author: Dusan Misevic and Antoine Frenoy and David P. Parsons and Francois Taddei Title: "Effects of public good properties on the evolution of cooperation" Booktitle: Proceedings of Artificial Life XIII Year: 2012 Pages: 218-225 Eprint: http://mitpress.mit.edu/sites/default/files/titles/content/alife13/978-0-262-31050-5-ch030.pdf URL: http://www.aevol.fr/publications/ Type: inproceedings - Author: Antoine Frenoy and Francois Taddei and Dusan Misevic Title: "Robustness and evolvability of cooperation" Booktitle: Proceedings of Artificial Life XIII Year: 2012 Pages: 53-58 Eprint: http://mitpress.mit.edu/sites/default/files/titles/content/alife13/978-0-262-31050-5-ch008.pdf URL: http://www.aevol.fr/publications/ Type: inproceedings - Author: Guillaume Beslon and David P. Parsons and Yolanda Sanchez-Dehesa and Jose Maria Pena and Carole Knibbe Title: "Scaling Laws in Bacterial Genomes: A Side-Effect of Selection of Mutational Robustness" Journal: BioSystems Year: 2010 Volume: 102 Number: 1 Pages: 32-40 URL: http://www.aevol.fr/publications/ Type: article - Author: David P. Parsons and Carole Knibbe and Guillaume Beslon Title: "Importance of the rearrangement rates on the organization of transcription" Booktitle: Proceedings of Artificial Life XII Year: 2010 Pages: 479-486 Eprint: http://mitpress.mit.edu/sites/default/files/titles/alife/0262290758chap92.pdf URL: http://www.aevol.fr/publications/ Type: inproceedings - Author: Carole Knibbe and Antoine Coulon and Olivier Mazet and Jean-Michel Fayard and Guillaume Beslon Title: "A long-term evolutionary pressure on the amount of noncoding DNA" Journal: Mol. Biol. Evol. Year: 2007 Volume: 24 Number: 10 Pages: 2344-2353 Eprint: http://mbe.oxfordjournals.org/content/24/10/2344.full.pdf+html?sid=9a6ee107-7aed-4750-8015-f8a2cc136cf9 URL: http://www.aevol.fr/publications/ Type: article