Data from: 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 empirical matrices and finite mixtures. The parallelization is
made efficient thanks to the combination of two algorithmic strategies: a
partial Gibbs sampling update of the tree topology, and the use of a
truncated stick-breaking representation for the Dirichlet process prior.
The implementation shows close to linear gains in computational speed for
up to 64 cores, thus allowing faster phylogenetic reconstruction under
complex mixture models. PhyloBayes MPI is freely available from our
website www.phylobayes.org.