biomc2 is a hierarchical Bayesian procedure to detect recombination in DNA sequence alignments based on the incongruence between topologies caused by recombinational events.
:: MORE INFORMATION
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.