SeqTrack algorithm Our method aims to reconstruct the transmission tree of pathogens during a disease outbreak, using genotypes and collection dates to uncover ancestries between sampled isolates. The fundamental innovation of our approach is to seek ancestors directly from the sampled isolates, rather than attempting to reconstruct unobserved and hypothetical ancestral genotypes. Because ancestries are in essence temporally oriented connections between isolates, it seemed natural to tackle the problem of inferring genealogies within graph theory.