Pinned Repositories
treeBreaker
Algorithm to divide a phylogenetic tree into segments based on phenotypes at the leaves of the tree
treeWAS
treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
skygrowth
Phylodynamic inference
BactDating
Bayesian inference of ancestral dates on bacterial phylogenetic trees
ClonalFrameML
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
ClonalOrigin
Inference of homologous recombination in bacteria using whole genome sequences
DetectImports
Detection of imports in a dated phylogeny
o2mod.transphylo
outbreaker2 module using the TransPhylo model
TransPhylo
Reconstruction of transmission trees using genomic data
TransPhyloMatlab
Inference of a pathogen transmission tree given a phylogeny
xavierdidelot's Repositories
xavierdidelot/ClonalFrameML
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
xavierdidelot/BactDating
Bayesian inference of ancestral dates on bacterial phylogenetic trees
xavierdidelot/TransPhylo
Reconstruction of transmission trees using genomic data
xavierdidelot/DetectImports
Detection of imports in a dated phylogeny
xavierdidelot/ClonalOrigin
Inference of homologous recombination in bacteria using whole genome sequences
xavierdidelot/TransPhyloMatlab
Inference of a pathogen transmission tree given a phylogeny
xavierdidelot/o2mod.transphylo
outbreaker2 module using the TransPhylo model
xavierdidelot/ARC-examples
xavierdidelot/campy
xavierdidelot/ClonalFrame
ClonalFrame: inference of recombination in bacteria
xavierdidelot/gonovax
xavierdidelot/SimBac
Source code for SimBac, a bacterial genome simulator
xavierdidelot/TransPairs
xavierdidelot/xavierdidelot.github.io
Website of Xavier Didelot