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

CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

(2013) Manuel Gil et al.   MOLECULAR BIOLOGY AND EVOLUTION

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

On the Statistical Interpretation of Site-Specific Variables in Phylogeny-Based Substitution Models

(2012) N. Rodrigue   GENETICS

Integrating Sequence Variation and Protein Structure to Identify Sites under Selection

(2012) Austin G. Meyer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models

(2011) A. U. Tamuri et al.   GENETICS

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

(2010) N. Rodrigue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Likelihood Analysis on Large Phylogenies Using Partial Sampling of Substitution Histories

(2009) A. P. J. de Koning et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage

(2008) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION