Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes

Benchmarking Multi-Rate Codon Models

(2010) Wayne Delport et al.   PLoS One

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

(2010) Wayne Delport et al.   PLoS Computational Biology

Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences

(2009) Tae-Kun Seo et al.   SYSTEMATIC BIOLOGY

Bayesian Comparisons of Codon Substitution Models

(2008) Nicolas Rodrigue et al.   GENETICS

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

(2008) M. Anisimova 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

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian analysis of amino acid substitution models

(2008) J. P Huelsenbeck et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Synonymous Substitutions Substantially Improve Evolutionary Inference from Highly Diverged Proteins

(2008) Tae-Kun Seo et al.   SYSTEMATIC BIOLOGY