Automated analysis of phylogenetic clusters. - Manon Ragonnet-Cronin; Emma B. Hodcroft; Stéphane Hué; Esther Fearnhill; Valerie Delpech; Andrew J. Leigh Brown; Samantha Lycett (BMC Bioinform., 2013)

Nextclade: clade assignment, mutation calling and quality control for viral genomes. - Ivan Aksamentov; Cornelius Roemer; Emma B. Hodcroft; Richard A. Neher (J. Open Source Softw., 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)

Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2. - Emma B. Hodcroft; Martin Wohlfender; Richard A. Neher; Julien Riou; Christian L. Althaus (PLoS Comput. Biol., 2025)