| Arlequin | windows/linux | An Integrated Software for Population Genetics Data Analysis | http://cmpg.unibe.ch/software/arlequin35/Arl35Downloads.html |
| BEAST | windows/mac/linux | BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences | http://beast.bio.ed.ac.uk/home |
| BEAUti | windows/mac/linux | BEAUti is a graphical user-interface (GUI) application for generating BEAST XML files | avec paquet BEAST |
| BioEdit | windows | BioEdit is a biological sequence alignment editor | http://www.mbio.ncsu.edu/bioedit/bioedit.html |
| Clustal | windows/mac/linux | Multiple alignment of nucleic acid and protein sequences | http://www.clustal.org/download/current/ |
| CREATE | windows | CREATE is software for the creation of new and conversion of existing data input files for 64 genetic data analysis software programs. | http://bcrc.bio.umass.edu/pedigreesoftware/node/2 |
| Ecogenetics | windows | offers a set of tools to study spatially-explicit metapopulations | https://www2.unil.ch/biomapper/ecogenetics/index.html |
| FigTree | windows/mac/linux | FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures | http://tree.bio.ed.ac.uk/software/figtree/ |
| Fstat | windows | FSTAT is a computer package for PCs which estimates and tests gene diversities and differentiation statistics from codominant genetic markers | https://www2.unil.ch/popgen/softwares/fstat.htm |
| Genepop | windows/mac/linux | GENEPOP is a population genetics software package | http://kimura.univ-montp2.fr/~rousset/Genepop.htm |
| Genetix | windows | permet le calcul d'un ensemble de paramètres couramment utilisés en génétique des populations, et propose l'étude de leur signification statistique par l'emploi de tests de ré-échantillonnage de type permutations | http://www.genetix.univ-montp2.fr/genetix/genetix.htm |
| jalview | windows/mac/linux | Jalview is a free programm developped for interactive editing, analysis and visualisation of multiple sequence alignments. | http://www.jalview.org/download/ |
| MEGA | windows/mac/linux | MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses | http://www.megasoftware.net/ |
| MeV | windows/mac/linux | MeV is a desktop application for the analysis, visualization and data-mining of large-scale genomic data | http://www.tm4.org/mev/ |
| MrBayes | windows/mac/linux | MrBayes is a program for the Bayesian estimation of phylogeny | http://mrbayes.csit.fsu.edu/download.php |
| NJplot | windows/mac/linux | NJplot is a tree drawing program able do draw any phylogenetic tree expressed in the Newick phylogenetic tree format | http://pbil.univ-lyon1.fr/software/njplot.html |
| PAML | windows | PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood | http://abacus.gene.ucl.ac.uk/software/paml.html |
| Paup | windows/mac/linux | tools for inferring and interpreting phylogenetic trees | http://paup.csit.fsu.edu/versions.html |
| PCAGEN | windows | PCAGEN is a computer package for windows wich perform Principal Component Analysis (PCA) on gene frequency data. | https://www2.unil.ch/popgen/softwares/pcagen.htm |
| Phylip | windows/mac/linux | PHYLIP is a free package of programs for inferring phylogenies | http://evolution.genetics.washington.edu/phylip/getme.html |
| PhyML | windows/mac/linux | PhyML is a phylogeny software based on the maximum-likelihood principle | http://www.atgc-montpellier.fr/phyml/binaries.php |
| Populus | windows/mac/linux | The Populus software contains a set of simulations to teach population biology and evolutionary ecology | http://www.cbs.umn.edu/populus/installer |
| R | windows/mac/linux | R is a free software environment for statistical computing and graphics | http://stat.ethz.ch/CRAN/ |
| SASDA | windows | allows to simulate and visualize the genetic and geographic evolution of a species on a continent under various climatic conditions | ? |
| SeaView | windows/mac/linux | SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny | http://pbil.univ-lyon1.fr/software/seaview.html |
| Structure | windows/mac/linux | The program structure is a free software package for using multi-locus genotype data to investigate population structure | http://pritch.bsd.uchicago.edu/structure.html |
| TCS | windows/mac/linux | TCS is a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks) | http://darwin.uvigo.es/software/tcs.html |
| Tinn-R | windows | editeur de texte spécifique pour R | http://sourceforge.net/projects/tinn-r/ |
| Tracer | windows/mac/linux | Tracer is a program for analysing the trace files generated by Bayesian MCMC runs | http://tree.bio.ed.ac.uk/software/tracer/ |
| TreeAnnotator | windows/mac/linux | This program assists in summarizing the information from a sample of trees produced by BEAST onto a single “target” tree | avec paquet BEAST |
