NGS Softwares Descriptions
PopPhyl Project The PopPhyl project provides a set of publicly available tools C++ code to achieve SNP and genotype calling (with home made algorithms). Also are provided wrappers to use this tools in the Galaxy platforms.
Sam2alr Sam2alr converter; C++ executable (Static compilation for 64 bits Linux) Bam2alr
Reads2SNP C++ executable (Static compilation for 64 bits Linux)
reads2snp_wrapper.pl Read2SNP Perl wrapper. (Multithreaded)
dNdSpiNpiS dNdSpiNpiS C++ executable (Static compilation for 64 bits Linux)
Site_frequency_spectr Site_frequency_spectr a C++ executable (Static compilation for 64 bits Linux)
Sam2alr XML wrapper for Galaxy XML file to use Sam2alr C++ executable in Galaxy
Bam2alr XML wrapper for Galaxy XML file to use Bam2alr C++ executable in Galaxy
Reads2SNP XML wrapper for Galaxy XML file to use Reads2SNP Perl wrapper in Galaxy
dNdSpiNpiS XML wrapper for Galaxy XML file to use dNdSpiNpiS C++ executable in Galaxy
Site_frequency_spectra XML wrapper for Galaxy XML file to use Site_frequency_spectra C++ executable in Galaxy

All source files and makefiles of the PopPhyl project C++ executables

POPULATION GENETICS Softwares Descriptions
Genepop Classical population genetic tests and various more focused applications (e.g. inferences under isolation by distance). For Windows and Linux.
IDENTIX1.1 Permutation test of relatedness
GENETIX v4.05 Set of population genetics programs
PARTITION Bayesian identification of population sub-division
PARTITION_ML Maximum Likelihood test of population sub-division
NEUTRALLELIX Monolocus Neutrality Test
SWEEP_BOTT Detecting bottlenecks and selective sweeps
DETSEL Program to detect markers responding to selection
KsimPop logiciel pédagogique, conçu pour permettre aux étudiants de construire des modèles de biologie des populations
PHYLOGENY & MOLECULAR EVOLUTION Softwares Descriptions
HGT_simul Program implementing the phylogenomic simulation procedure described in: Galtier N. 2007. A model of horizontal gene transfer and the bacterial phylogeny problem. Systematic Biology (in press).
PHYLO_WIN v1.2 Graphical interface to molecular phylogeny
NHML v3 Non-homogeneous maximum likelihood for phylogenetics
BAOBAB Program for editing and displaying large trees
CoMap A C++ shell program to detect co-evolving groups of sites
PhyloExplorer 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.
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.
CODE LIBRARIES & OTHER TOOLS Descriptions
BioPP Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics
Bio ++ Program Suite A set of programs for phylogenetic trees rec