Xavier Didelot

ClonalFrameML. ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

BactDating. Bayesian inference of ancestral dates on bacterial phylogenetic trees

TransPhylo. Reconstruction of transmission trees using genomic data

DetectImports. Detection of imports in a dated phylogeny

ClonalOrigin. Inference of homologous recombination in bacteria using whole genome sequences

DiagnoDating. Diagnostics for dated phylogenies in microbial population genetics

TransPhyloMatlab. Inference of a pathogen transmission tree given a phylogeny

EpiLambda. TeX

GenoPlast. Inference of genomic gain and loss in prokaryotes

ClonalFrame. ClonalFrame: inference of recombination in bacteria

o2mod.transphylo. outbreaker2 module using the TransPhylo model

TransPairs. MATLAB