ISDB: a database toolkit for storing and analyzing viral integration site data. - Thomas R. Sibley; Evan J. Silberman; James I. Mullins (Bioinform., 2019)

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)

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)