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  • Arlequin  •  Arlequin provides the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. The graphical interface is designed to allow users to rapidly select the different analyses they want to perform on their data. One can explore the data, and analyze several times the same data set from different perspectives, with different selected options. [less]
  • BayeScan  •  BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model. [less]
  • CT-CBN  •  Continuous time conjunctive Bayesian networks (ct-cbn) are a family of graphical models describing the accumulation of mutations under order constraints. The software allows for the estimation of the network from cross-sectional data, such as mutation profiles of cancer or HIV patients.  [less]
  • fastsimcoal  •  fast sequential markov coalescent simulation of genomic data under complex evolutionary models [less]
  • mOTUs  •  The mOTUs tool uses phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) to profile microorganisms at species-level resolution when using metagenomic data as input. Since the MGs represent housekeeping genes, mOTUs can also be used to profile transcriptionally active community members when using metatranscriptomic data as input. Furthermore, MG-based SNV profiling provides an efficient alternative to using whole genome sequences to compare microbial strain populations. [less]
  • TriFLe  •  TRiFLe is a program for simulating TRFs and identifying species by TRF profiling [less]
  • V-Pipe  •  V-pipe is a bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. [less]