I have contributed to the development of the following computer software, all of which are freely available on the internet:
- ClonalFrame (2007): a phylogenetic method that detects and accounts for bacterial recombination
- GenoPlast (2009): analysis of genomic plasticity in bacteria
- SimMLST (2009): simulation of genetic data under a neutral model
- ClonalOrigin (2010): inference of bacterial recombination including ancestral donors and recipients
- TransPhylo (2014): inference of host-to-host transmission using genomic data
- ClonalFrameML (2015): efficient inference of recombination in whole bacterial genomes
- treeBreaker (2016): analysis of phenotypic distribution on a phylogenetic tree
- SimBac (2016): scalable simulation of whole bacterial genomes with homologous recombination
- skygrowth (2017): phylodynamic analysis of microbial growth rate over time
- treeWAS (2018): a phylogenetic method to perform Genome-Wide Association Studies (GWAS) in microbes
- BactDating (2018): inference of dated phylogenies in bacterial genomics
- simdynet (2019): realistic simulation of dynamic sexual networks
- treestructure (2020): Identification of hidden population structure in time-scaled phylogenies
- mlesky (2022): maximum-likelihood inference of pathogen population size history