Logiciels
De nombreux chercheurs et ingénieurs du CBGP ont développé et continuent de développer des méthodes d’analyse originales en génétique et génomique des populations, en phylogénie et phylogénomique, mais aussi en écologie. Ces méthodes et ces modèles sont mis à la disposition de la communauté sous la forme de logiciels, de scripts et de paquetages R, le plus souvent protégés par des licences publiques ouvertes. N’hésitez pas à les utiliser !
BayPass
Genome-Wide Scan for Adaptive Differentiation and Association Analysis with population-specific covariables
Bottleneck
An integrated software for detecting recent variations in effective population size from allele frequency data
DetSel
An 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-RF
An inference software implementing Approximate Bayesian Computation (ABC) combined with supervised machine learning based on Random Forests (RF), for model choice and parameter inference in the context of population genetics analysis
FreeNA
A computer program that allows various statistical treatments on microsatellite datasets with null alleles
GeneClass2
A program employing multilocus genotypes to select or exclude populations as origins of individuals (Assignment and Migrants Detection)
IBDSim
Simulation of genotypic data under general isolation by distance models
JMS-v1
A computer program for a simulation-based evaluation of the diagnostic status of juxtaposed microsatellite systems
KimTree
A software package implementing a hierarchical Bayesian model to estimate divergence times (in a diffusion time scale) in a population tree, from large single nucleotide polymorphism (SNP) data
MAPI
A -R- package delivering 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
Migraine
Coalescent algorithms for maximum likelihood analysis of population genetic data
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 Extended Haplotype Homozygosity based tests
SelEstim
Detecting and measuring selection from gene frequency data
|SE|S|AM|E| Barcode
A user-friendly web application for barcoding amplicon sequences obtained through NGS
ECPaysage
A set of R resources to teach landscape ecology, landscape analysis and spatial statistics
RADIS
Analysis of RAD-seq data for interspecific phylogeny
