Figure 1. Illustration of possible reconstructions of genealogical relations. Panel a represents a hypothetical genealogy of five strains from which three were sampled (highlighted by a blue glow). Panel b and c illustrate phylogenetic reconstructions where the red dots represent inferred nodes; panel b corresponds to a classical phylogenetic reconstruction and c to a tree that accounts for heterochronous sampling (e.g. Beast software [8]). Panel d illustrates the direct ancestry reconstruction method implemented in SeqTrack.  While none of the methods recovers the correct genealogy (panels b-d), the best reconstruction is provided by SeqTrack in this example (panel d).