Phandango: an interactive viewer for bacterial population genomics. - James Hadfield; Nicholas J. Croucher; Richard J. Goater; Khalil AbuDahab; David M. Aanensen; Simon R. Harris (Bioinform., 2018)

Nextstrain: real-time tracking of pathogen evolution. - James Hadfield; Colin Megill; Sidney M. Bell; John Huddleston; Barney Potter; Charlton Callender; Pavel Sagulenko; Trevor Bedford; Richard A. Neher (Bioinform., 2018)

High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. - Rafaela S. Fontenele; Simona Kraberger; James Hadfield; Erin M. Driver; Devin Bowes; LaRinda A. Holland; Temitope O. Faleye; Sangeet Adhikari; Rahul Kumar; Rosa Inchausti; Wydale K. Holmes; Stephanie Deitrick; et al. (AMIA, 2021)

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. - John Huddleston; James Hadfield; Thomas R. Sibley; Jover Lee; Kairsten Fay; Misja Ilcisin; Elias Harkins; Trevor Bedford; Richard A. Neher; Emma B. Hodcroft (J. Open Source Softw., 2021)

RCandy: an R package for visualizing homologous recombinations in bacterial genomes. - Chrispin Chaguza; Gerry Tonkin-Hill; Stephanie W. Lo; James Hadfield; Nicholas J. Croucher; Simon R. Harris; Stephen D. Bentley (Bioinform., 2022)

Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition. - Jover Lee; James Hadfield; Allison Black; Thomas R. Sibley; Richard A. Neher; Trevor Bedford; John Huddleston (Frontiers Bioinform., 2023)