SeqTrack is a very versatile approach that allows for weighting the plausibility of individual ancestries in various ways. In this study, we used a maximum parsimony version of the method because the origin of A/H1N1 influenza virus is sufficiently recent for homoplasies (recombination or back mutations) to be very unlikely, and safely ignored. Nonetheless, SeqTrack genealogies could be optimized on other criteria, such as genetic distances or log-likelihoods based on complex models of sequence evolution. Another possible extension of this method relates to the use of heterogeneous genetic information, which occurs when the regions of the genome sequenced vary across isolates. Such heterogeneity is likely to occur as soon as the sequencing effort is undertaken independently by a large number of labs, as was the case during the early stage of the 2009 A/H1N1 influenza pandemic. As a result, sequence data of the new influenza strain consisted of essentially random combinations of segments, ranging from small fragments of specific genes to whole genomes. In such cases, the analysis of homologous sequences results in a possibly considerable loss of information. This issue could be overcome by averaging genetic differentiation across available segments, using appropriate weights to account for different substitution rates and segment lengths. However, including a large fraction of isolates with heterogeneous sequencing coverage would require accurate estimates of substitution rates, which can be difficult to obtain for emerging pathogens.