Empirical profile mixture models for phylogenetic reconstruction

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 with their finite counterparts, infinite mixtures have a greater expressivity. However, they...

PhyloBayes 3.3 a Bayesian software for phylogenetic reconstruction and molecular dating using mixture models

PhyloBayes-MPI A Bayesian software for phylogenetic reconstruction using mixture models MPI version

Pitfalls of heterogeneous processes for phylogenetic reconstruction.

Different genes often have different phylogenetic histories. Even within regions having the same phylogenetic history, the mutation rates often vary. We investigate the prospects of phylogenetic reconstruction when all the characters are generated from the same tree topology, but the branch lengths vary (with possibly different tree shapes). Furthering work of Kolaczkowski and Thornton (2004, N...

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

MOTIVATION A variety of probabilistic models describing the evolution of DNA or protein sequences have been proposed for phylogenetic reconstruction or for molecular dating. However, there still lacks a common implementation allowing one to freely combine these independent features, so as to test their ability to jointly improve phylogenetic and dating accuracy. RESULTS We propose a software ...