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Logiciels spécialisés

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/Main_Page
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
http://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
http://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.
http://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
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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


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