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/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

 

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