PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment

Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed, and have been shown to significantly improve on classical single-matrix models. Compared to their finite counterparts, infinite mixtures have a greater expressivity. However, they are computationally more challenging. This has resulted in practical compromises in the design of infinite mixture models. In particular, a fast but simplified version of a Dirichlet process model over equilibirum frequency profiles implemented in PhyloBayes (Lartillot et al, 2007) has often been used in recent phylogenomics studies, while more refined model structures, more realistic and empirically more fit, have been practically out of reach. We introduce an Message Passing Interface (MPI) version of PhyloBayes, implementing the Dirichlet process mixture models as well as more classical empiric...