title: Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package.
abstract: BACKGROUND
  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-based Bayesian implementation of site-heterogeneous codon models in the mutation-selection framework. Our software jointly infers the global mutational parameters at the nucleotide level, the branch lengths of the tree and a Dirichlet process governing across-site variation at the amino acid level. We focus on an example estimation of the distribution of selection coefficients from an alignment of several hundred sequences of the influenza PB2 gene, and highlight the site-specific characterization enabled by such a modeling approach. Finally, we discuss future potential applications of the software for conducting evolutionary inferences.
  
  
  METHODS
  The models are implemented within the PhyloBayes-MPI package, (available at phylobayes.org) along with usage details in the accompanying manual.
authors.affiliation: Department of Mathematics and Statistics, University of Calgary, 2500 University Drive NW, Calgary AB T2N 1N4, Canada and UMR CNRS 5558 - LBBE, Université Lyon 1, Villeurbanne Cedex, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Rodrigue
authors.forename: Nicolas
authors.initials: N
authors.lastname: Lartillot
mesh_terms: D001499:Bayes Theorem; D003062:Codon; D008957:Models, Genetic; D009154:Mutation; D010802:Phylogeny; D012984:Software
chemical_list: D003062:Codon