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