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
(2014,2017,2021): inference of host-to-host transmission using genomic
data
- ClonalFrameML
(2015): efficient inference of recombination in whole bacterial
genomes
- SimBac (2016):
scalable simulation of whole bacterial genomes with homologous
recombination
- treeBreaker
(2016): analysis of phenotypic distribution on a phylogenetic tree
- treeWAS
(2018): a phylogenetic method to perform Genome-Wide Association Studies
(GWAS) in microbes
- skygrowth (2018):
phylodynamic analysis of microbial growth rate over time
- 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
- DetectImports
(2022): detecting imports in genomic samples from a local
population
- mlesky
(2023): maximum-likelihood inference of pathogen population size
history
- KmerAperture
(2024): retaining k-mer synteny for alignment-free extraction of core
and accessory differences
- KPop (2025):
accurate and scalable comparative analysis of microbial genomes by
sequence embedding
- EpiLambda
(2025): ancestral process for infectious disease outbreaks with
superspreading
- DiagnoDating
(2026): diagnostics of dated phylogenies in microbial population
genetics