A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

(2010) Sergei Kosakovsky Pond et al.   PLoS One

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

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

(2010) Wayne Delport et al.   PLoS Computational Biology

Evolutionary Fingerprinting of Genes

(2009) S. L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

(2009) M. Nozawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and Its Application to Influenza A Virus

(2008) S. L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Frequent Toggling between Alternative Amino Acids Is Driven by Selection in HIV-1

(2008) Wayne Delport et al.   PLoS Pathogens