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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

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

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

Learning to Count: Robust Estimates for Labeled Distances between Molecular Sequences

(2009) J. D. O'Brien et al.   MOLECULAR BIOLOGY AND EVOLUTION

Computational Methods for Evaluating Phylogenetic Models of Coding Sequence Evolution with Dependence between Codons

(2009) N. Rodrigue et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

Independent Origins of New Sex-Linked Chromosomes in the melanica and robusta Species Groups of Drosophila

(2008) Sergio V Flores et al.   BMC EVOLUTIONARY BIOLOGY

Models of coding sequence evolution

(2008) W. Delport et al.   BRIEFINGS IN BIOINFORMATICS

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

Bayesian analysis of amino acid substitution models

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

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes

(2008) M. T Holder et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences

(2008) S. C. Choi et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

(2008) S. Yokoyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synonymous Substitutions Substantially Improve Evolutionary Inference from Highly Diverged Proteins

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

A Model-Based Approach to Study Nearest-Neighbor Influences Reveals Complex Substitution Patterns in Non-coding Sequences

(2008) Guy Baele et al.   SYSTEMATIC BIOLOGY

Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci

(2008) Chenhong Li et al.   SYSTEMATIC BIOLOGY