Our latest article has just been published in Systematic Biology. It describes a model for estimating the set of species trees conforming to several tree-to-tree distances at once. We show how we can use reconciliation distances, the recently developed mulRF distance, or a combination of them into a single multivariate distribution that is incorporated into a hierarchical Bayesian model. We then conduct extensive simulations and show how our method performs well even when we have paralogy and deep coalescences at once.
We implemented this model into the software guenomu, which is available under a GPL license at http://bitbucket.org/leomrtns/guenomu.
Leonardo De Oliveira Martins, Diego Mallo and David Posada (2014). A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Systematic Biology, in press, doi: 10.1093/sysbio/syu082