To circumvent this problem, we introduce a new methodological approach for the analysis of genetic data collected during disease outbreaks. Contrary to phylogenetic methods, we consider that sampled isolates represent a fraction of the genealogy, including internal nodes and tips (Figure 1d ). Direct and indirect ancestries can therefore be inferred between the sampled isolates. Within this framework, we developed an algorithm called SeqTrack, which directly reconstructs the most plausible genealogy of a set of sampled isolates, allowing for a direct assessment of the spatiotemporal dynamics of the epidemic under study.