Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. - Sergei L. Kosakovsky Pond; Simon D. W. Frost (Bioinform., 2005)

HyPhy: hypothesis testing using phylogenies. - Sergei L. Kosakovsky Pond; Simon D. W. Frost; Spencer V. Muse (Bioinform., 2005)

GARD: a genetic algorithm for recombination detection. - Sergei L. Kosakovsky Pond; David Posada; Michael B. Gravenor; Christopher H. Woelk; Simon D. W. Frost (Bioinform., 2006)

Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses. - Sergei L. Kosakovsky Pond; Simon D. W. Frost; Zehava Grossman; Michael B. Gravenor; Douglas D. Richman; Andrew J. Leigh Brown (PLoS Comput. Biol., 2006)

Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope. - Art F. Y. Poon; Fraser I. Lewis; Sergei L. Kosakovsky Pond; Simon D. W. Frost (PLoS Comput. Biol., 2007)

An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope. - Art F. Y. Poon; Fraser I. Lewis; Sergei L. Kosakovsky Pond; Simon D. W. Frost (PLoS Comput. Biol., 2007)

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. - Art F. Y. Poon; Fraser I. Lewis; Simon D. W. Frost; Sergei L. Kosakovsky Pond (Bioinform., 2008)

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1. - Sergei L. Kosakovsky Pond; David Posada; Eric W. Stawiski; Colombe Chappey; Art F. Y. Poon; Gareth Hughes; Esther Fearnhill; Mike B. Gravenor; Andrew J. Leigh Brown; Simon D. W. Frost (PLoS Comput. Biol., 2009)

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. - Wayne Delport; Art F. Y. Poon; Simon D. W. Frost; Sergei L. Kosakovsky Pond (Bioinform., 2010)

Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection. - Erik M. Volz; James S. Koopman; Melissa J. Ward; Andrew J. Leigh Brown; Simon D. W. Frost (PLoS Comput. Biol., 2012)

Inferring the Source of Transmission with Phylogenetic Data. - Erik M. Volz; Simon D. W. Frost (PLoS Comput. Biol., 2013)

Measuring Asymmetry in Time-Stamped Phylogenies. - Bethany L. Dearlove; Simon D. W. Frost (PLoS Comput. Biol., 2015)

Gillespie.jl: Stochastic Simulation Algorithm in Julia. - Simon D. W. Frost (J. Open Source Softw., 2016)

genieR: An R package for inference of demographic history of phylogenies. - Fei Xiang; Bethany L. Dearlove; Simon D. W. Frost (J. Open Source Softw., 2019)