Genetics

• Baypass. The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).

• Bottleneck. An integrated software for detecting recent variations in effective population size from allele frequency data.

• DetSel. A R package to detect markers responding to selection.

• DetSex. A software to assign marker to their chromosome type and to perform sexing of individuals using genotyping data.

• DIYABC. An integrated software with a user-friendly graphical interface to infer complex population histories using Approximate Bayesian Computation (ABC) from single nucleotide polymorphism (SNP), DNA sequence and microsatellite data.

• FreeNA. A computer program that allows various statistical treatments on microsatellite datasets with null alleles.

• ggene. An R package dedicated to the geostatistical analysis of microsatellite data recorded for geolocated individuals.

• GeneClass2. An integrated software to assign individuals to populations based on multilocus genotypes.

• IBDSim. A software to simulate genotypic data from general isolation by distance models.

• JMS-v1. A computer program for a simulation-based evaluation of the diagnostic status of juxtaposed microsatellite systems in the context of genetic introgression.

• Kim Tree. A program aimed at estimating divergence times on a diffusion time scale from large single nucleotide polymorphism (SNP) data.

• MAPI. An exploratory and visual method providing geographical representations summarizing the spatial variation of pairwise metrics (e.g. distance, similarity coefficient, etc.) computed between georeferenced samples.  Data storage and spatial treatments are done under PostgreSQL with Postgis extension enabled.  Cartographic representation of MAPI results can be done under GIS software such as QGis.

• Migraine. A software that implements maximum likelihood analysis of population genetic data based on coalescent algorithms.

• PoolSeqUtils. A suite of programs to facilitate the experimental design procedure and to perfom quality check of Pool-Seq data.

• Rehh. A R package to search for footprints of selection using Haplotype Homozygosity based tests.

• SelEstim. A software to detect signatures of selection from gene frequency data and measure the selection intensity.

• |SE|S|AM|E| Barcode. A user-friendly web application for barcoding amplicon sequences obtained through NGS. The software automatically processes DNA sequences datasets, sorting for multiplexed loci and samples identified by oligonucleotide tags, and allows for the assignment of sequences to a preloaded reference library (from Genbank to in-house scale). The results are displayed both as samples-based synthetic tables and graphical representations. The deliveries of |SE|S|AM|E| Barcode are though with multiple applications in mind, such as specimen assignment to species referenced in DNA libraries, molecular characterization of trophic networks or more generally metagenomics and environmental barcoding studies.

Ecology

• ECPaysage. A set of R resources to teach landscape ecology, landscape analysis and spatial statistics.

• rich is dedicated to the analysis of species richness and allows to perform bootstrap estimation of species richness, compare richnesses and compute rarefaction curves.

Phylogeny

• RADIS. An attempt to make the processing of RAD-seq data easier and allow rapid and automated exploration of parameters/data for phylogenetic inference, we developed the perl pipeline RADIS.

Galaxy tools