 We developed a phylogenetic pipeline that uses both full and partial viral genome sequences to study the spread of viruses over time. The pipeline was applied to Rabi's virus, RABV, which revealed an emergence of the current canine-mediated strain around year 1301 and multiple regional introductions over a 700-year period. This enabled us to identify episodes of human-mediated introductions of RABV and explore how European colonization influenced its spread. The pipeline also allowed us to analyze large and genetically diverse datasets for many viral pathogens. This article was authored by Andrew Holtz, Guy Bale, Heve Pohi, and others.