Fig. 5

BAsE-Seq approximately maximum-likelihood trees of viral sequences from P2 (a), P7 (b), P1 (c), and P11 (d). Tip label colors indicate if the viral sequence came from before (black) or after (orange) drug resistance. 100 sub-sampled sequences from each timepoint are used, color-coded by their branch labels. Bootstrap values are reflected in branch color, ranging between 0 (red) to 1 (green). Blue arrows indicate emergence of resistance mutations. For a full phylogeny of all sequences, refer to (Additional file 1 Figures 14–17)