Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

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

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

(2009) Sergei L. Kosakovsky Pond et al.   PLoS Computational Biology

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models

(2008) A. F. Y. Poon et al.   BIOINFORMATICS

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