Simulation results showed fundamental differences between the SeqTrack algorithm and classical phylogenetic reconstruction (Figures 2 and 3) . In two randomly chosen examples, SeqTrack reconstructed very satisfyingly the transmission tree of the isolates (Figures 2b and  3b ). When all isolates were sampled, the method perfectly identified the transmission tree ( Figure 2b ). However, results remained very satisfying in the incompletely sampled genealogy (Figure 3b ), in which SeqTrack correctly inferred the most recent sampled ancestors, and therefore true branches of the transmission tree. In contrast, phylogenetic trees could hardly be used to draw inferences about the underlying genealogies (Figures 2c and 3c) . Indeed, the phylogenetic trees were not a good match to the transmission tree, and contained some oddities such as several identical internal nodes for a single polytomy (Figures 2c and  3c ). Even when considering tips with zero branch length as internal nodes, the resulting inferred ancestries were largely erroneous. Results obtained by BEAST were somewhat more satisfying, as the tips were ordered according to the sampling time. However, BEAST failed to identify any of the direct ancestries present in the simulated data set (Figures 2d and 3d) .