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

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 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 ...

Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

MOTIVATION In recent years, there has been an increasing interest in the potential of codon substitution models for a variety of applications. However, the computational demands of these models have sometimes lead to the adoption of oversimplified assumptions, questionable statistical methods or a limited focus on small data sets. RESULTS Here, we offer a scalable, message-passing-interface-b...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

SUMMARY TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964-969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has ...