Figure 1.

Examples of simulated trees. Four examples of trees extracted from our simulated data sets. Trees a) and c) are intended to simulate inter-host evolution of HIV (one tip per host; 750/1000 of the strains are removed at each sampling date). Trees b) and d) are intended to simulate intra-host evolution of HIV, with its typical “ladder shape” (all tips from a single host; 995/1000 of the strains are removed at each sampling date). Trees a) and b) have each 3 sampling dates with 25 sampled strains each. Trees c) and d) have each 11 sampling dates with 10 sampled strains each. See text and Volz et al. (2013) for explanations.