Codonphyml: Fast maximum likelihood phylogeny estimation under codon substitution models

Marcelo Serrano Zanetti, Manuel Gil, Stefan Zoller and Maria Anisimova

Molecular Biology and Evolution (2013)


Recently, Markov models of codon substitution have come into the spotlight. By incorporating the structure of the genetic code and the selection intensity at the protein level they provide a more realistic representation of protein-coding sequences than nucleotide or amino acid models. Thus, for protein-coding genes phylogenetic inference is expected to be more accurate under codon models. So far, phylogeny reconstruction under codon models has been elusive due to computational difficulties of dealing with high dimension matrices. Here we present a fast maximum likelihood package for phylogenetic inference, CodonPhyML offering hundreds of different codon models, the largest variety to date, for phylogeny inference by maximum likelihood. CodonPhyML is tested on simulated and real data, and is shown to offer excellent speed and convergence properties. In addition, CodonPhyML includes most recent fast methods for estimating phylogenetic branch supports, and provides an integral framework for models selection, including amino acid and DNA models.