CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models.

ABSTRACT: Markov models of codon substitution naturally incorporate the structure of the genetic code and the selection intensity at the protein level, providing a more realistic representation of protein-coding sequences compared with 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 (ML) package for phylogenetic inference, CodonPhyML offering hundreds of different codon models, the largest variety to date, for phylogeny inference by ML. CodonPhyML is tested on simulated and real data and is shown to offer excellent speed and

SUBMITTER: Gil M 

PROVIDER: S-EPMC3649670 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature