References

MicrobeTrace is based on HIV-TRACE, which is described in

Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. 2018 Jan 31. HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens. Mol. Biol. Evol. doi:10.1093/molbev/msy016.