PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating.
BACKGROUND
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 package, PhyloBayes 3, which can be used for conducting Bayesian phylogenetic reconstruction and molecular dating analyses, using a large variety of amino acid replacement and nucleotide substitution models, including empirical mixtures or non-parametric models, as well as alternative clock relaxation processes.
Lartillot
Nicolas
N
Département de Biochimie, Université de Montréal, Montréal, Québec, Canada. nicolas.lartillot@umontreal.ca
Lepage
Thomas
T
Blanquart
Samuel
S
D000818:Animals; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D010802:Phylogeny; D011237:Predictive Value of Tests; D015203:Reproducibility of Results; D012984:Software; D013997:Time Factors