New article describing the "penalty function"

posted Jul 2, 2010, 5:37 AM by Leonardo de Oliveira Martins
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

I wrote some more info at this blog post.