Using simple simulations, we illustrate the major difference between phylogenetic methods and our approach, showing the advantage of SeqTrack over traditional phylogenetic approaches for inferring transmission trees in densely sampled disease outbreaks. We then evaluate the performance of our method using spatially explicit simulations of outbreaks. Finally, we illustrate the novel methodology using sequence data from the early stages of the 2009 A/H1N1 influenza pandemic, and reconstruct the likely scenario of worldwide spread of this newly emerged pathogen.