Génétique des populations, Biostatistiques

  • GENEPOP. Latest version of Genepop (Rousset 2008). Also available is a recompiled version of the linkdos program (Garnier-Géré and Dillmann 1992), which was distributed with previous versions of Genepop (Resp: F. Rousset)
  • GENEPOP v3.4. Last version of the classic (Raymond & Rousset, 1995) (Resp: M. Raymond, F. Rousset)
  • MIGRAINE implements some coalescent methods for likelihood inferences in population genetics (Resp: F. Rousset, R. Leblois)
  • IBDSim simulates samples under models of isolation by distance. Go to Raphaël Leblois’s page for more information (Resp: R. Leblois, F. Rousset).
  • GENETIX v4.05 is a set of population genetics programs (Resp: K. Belkhir, F. Bonhomme)
  • DETSEL, program to detect markers responding to selection (Resp: R. Vitalis, K. Belkhir)
  • IDENTIX1.1, a permutation test of relatedness
  • PARTITION, Bayesian identification of population sub-division (Resp: K. Belkhir,  K. J. Dawson)
  • PARTITION_ML, Maximum Likelihood test of population sub-division (Resp: K. Belkhir, F. Bonhomme)
  • NEUTRALLELIX, Monolocus Neutrality Test (Resp: N. Raufaste, F. Bonhomme)
  • T-LEX is a computational tool for a fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements (TEs) using Next-Generation Sequencing (NGS) data (Resp: A.S. Fiston-Lavier)

Phylogénétique, Phylo-informatique, Évolution moléculaire

  • HGT_simul, program implementing the phylogenomic simulation procedure described in: Galtier N. 2007. A model of horizontal gene transfer and the bacterial phylogeny problem (Resp: N. Galtier)
  • PHYLO_WIN v1.2, graphical interface to molecular phylogeny (Resp: N. Galtier)
  • NHML v3, non-homogeneous maximum likelihood for phylogenetics (Resp: N. Galtier)
  • BAOBAB, program for editing and displaying large trees (Resp: J. Dutheil)
  • CoMap, a C++ shell program to detect co-evolving groups of sites (Resp: J. Dutheil)
  • PhyloExplorer,  is a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database (Resp: V. Ranwez)
  • Macse. MACS_E, a multiple sequence alignment program dedicated to coding DNA sequences. MACS_E is able to handle some sequences errors and is thus especially adapted to align reads or EST together with more reliable sequences (Resp: V. Ranwez, E. Douzery)
  • OrthoMaM (Resp: V. Ranwez, F. Delsuc, E. Douzery) is a database of orthologous genomic markers for placental mammal phylogenetics now contains more than 6,000 exons and 12,000 CDSs. More details are available in the Open Access (BMC) paper (Resp: V. Ranwez, E. Douzery)
  • PhySIC_IST web server reconstructs topologies that are induced and not contradicted by source trees. More details about the approach are available in the Open Access (BMC) paper. This method ameliorates the initial PhySIC algorithm (Resp: C. Scornavacca, E. Douzery, V. Ranwez)

Bibliothèques de code et autres outils

  • The Bio++ project  is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. These C++ libraries are used in the Bio++ Program Suite that proposes a set of programs for phylogenetic trees reconstruction. It newly incorporates non-homogeneous models of sequence evolution (More details are available in the Open Access (BMC) paper) (Resp: J. Dutheil)
  • BioPP is a set of programs for phylogenetic trees reconstruction (Resp: J. Dutheil)

Bioinformatique

  • Montpellier Bioinformatics Biodiversity platform is a joint initiative of laboratories within the IFR 119 « Montpellier Environnement Biodiversité ». Its goal is to stimulate/coordinate research, developments and training in the fields of theoretical and computational ecology and evolution (Resp: K. Belkhir)
  • Cluster Gateway