PyEvolve: a toolkit for statistical modelling of molecular evolution. - Andrew Butterfield; Vivek Vedagiri; Edward Lang; Cath Lawrence; Matthew J. Wakefield; Alexander Isaev; Gavin A. Huttley (BMC Bioinform., 2004)

Vestige: Maximum likelihood phylogenetic footprinting. - Matthew J. Wakefield; Peter Maxwell; Gavin A. Huttley (BMC Bioinform., 2005)

A Probabilistic Method to Identify Compensatory Substitutions for Pathogenic Mutations. - B. C. Easton; A. V. Isaev; Gavin A. Huttley; Peter Maxwell (APBC, 2007)

Comparison of methods for estimating the nucleotide substitution matrix. - Maribeth Oscamou; Daniel McDonald; Von Bing Yap; Gavin A. Huttley; Manuel E. Lladser; Rob Knight 001 (BMC Bioinform., 2008)

Pathological rate matrices: from primates to pathogens. - Harold W. Schranz; Von Bing Yap; Simon Easteal; Rob Knight 001; Gavin A. Huttley (BMC Bioinform., 2008)

A comparison of periodicity profile methods for sequence analysis. - Manas Bellani; Julien Epps; Gavin A. Huttley (GENSiPS, 2012)

q2-sample-classifier: machine-learning tools for microbiome classification and regression. - Nicholas A. Bokulich; Matthew R. Dillon; Evan Bolyen; Benjamin D. Kaehler; Gavin A. Huttley; J. Gregory Caporaso (J. Open Source Softw., 2018)

GraphBin-Tk: assembly graph-based metagenomic binning toolkit. - Vijini Mallawaarachchi; Anuradha Wickramarachchi; Robert McArthur; Yapeng Lang; Katherine Caley; Gavin A. Huttley (J. Open Source Softw., 2025)