Evolutionary pathways of 273 PR genes (a) and 287 RT genes (b) from Patient 1 inferred using vSPA. Sampling time points A, B, ..., O are indicated on the horizontal axis, as well as the drug combination (DC) executed. The ellipses represent viral clusters inferred by the vSPA method. The clusters are ordered by the number of sequences they contain and are colored according to their frequencies. For example, at time point A, A1 has the most sequences among the clusters A, A2, ..., A7. Black arrows indicate the inferred evolutionary pathway. Important drug-resistant mutations are indicated on the pathway and the subpopulations divided according to the drug-resistant mutation are enclosed with dotted lines.