ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML was created by Xavier Didelot and Daniel Wilson. The software can be applied to any type of aligned nucleotide sequence data, but is especially aimed at analysis of whole genome sequences. It is able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. There are three main outputs from a run of ClonalFrameML: a phylogeny with branch lengths corrected to account for recombination, an estimation of the key parameters of the recombination process, and a genomic map of where recombination took place for each branch of the phylogeny.
ClonalFrameML is a maximum likelihood implementation of the Bayesian software ClonalFrame which was previously described by Didelot and Falush (2007). The recombination model underpinning ClonalFrameML is exactly the same as for ClonalFrame, but this new implementation is a lot faster, is able to deal with much larger genomic dataset, and does not suffer from MCMC convergence issues. A scientific paper describing ClonalFrameML in detail has been published, see Didelot X, Wilson DJ (2015) ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. PLoS Comput Biol 11(2): e1004041. doi:10.1371/journal.pcbi.1004041.
The project homepage for ClonalFrameML is clonalframeml.googlecode.com. You can obtain the most recent version of ClonalFrameML by downloading and compiling the C++ source code via SVN using the command:
svn checkout http://clonalframeml.googlecode.com/svn/trunk/ clonalframeml
From here you can download ready-to-use executables, a snapshot of the source code, and example data.