biomc2 is a hierarchical Bayesian procedure to detect recombination
in DNA sequence alignments based on the incongruence between topologies caused by recombinational events.
Please check out the accompanying blog for the software, where informal discussions and
announcements take place. You can also use the blog to send requests, questions and complains.
The software is released under the GPL license, and is now being hosted at github (not any more on google code): https://code.google.com/p/biomcmc. It can also be found in
the download area. Installation and further instructions can be found here.
The software is described in the following publications
Leonardo de Oliveira Martins, Élcio Leal and Hirohisa Kishino (2008) Phylogenetic Detection of Recombination with a Bayesian Prior on
the Distance between Trees. PLoS ONE 3(7): e2651.
Leonardo de Oliveira Martins and Hirohisa Kishino (2010) Distribution of distances between topologies and its effect on detection of phylogenetic recombination. Annals of the Institute of Statistical Mathematics 62(1): 145--159.
doi:10.1007/s10463-009-0259-8 [link to personal copy]
Leonardo de Oliveira Martins (2008) Bayesian Inference of Viral Recombination: Topology distance between DNA segments and its distribution. Ph.D. Thesis submitted to the Department of Agricultural and Environmental Biology of the Graduate School of Agricultural and Life Sciences of the The University of Tokyo.