Welcome to my software page. All programs are freely available to download.

BASTA, a method for fast and accurate phylogeography described in De Maio, Wu, O'Reilly and Wilson (2015) can be downloaded as a package for BEAST2. The coalescent methods for estimating parameters from SI, SIS and SIR epidemiological models described in Dearlove and Wilson (2013) can be downloaded as part of the latest version of BEAST. Please follow the links for all other programs below.

Virulogenomics

 

ClonalFrameML

 

gammaMap

Software pipeline for genome wide association studies (GWAS) in bacteria.   Efficient inference of recombination in bacterial genomes.   Estimate the distribution of fitness effects and localize the signal of selection.
   

omegaMap

 

iSource

 

xAMOVA

A program for detecting natural selection in the presence of recombination.   Tracing the source of transmission for bacterial multi-locus sequence typing.   Analysis of molecular variance for crossed designs.