Phylogenetic analysis of the <i>pol</i> alignment (Dataset 4).

<p>Evolutionary relationships were inferred with the use of the GTR model of nucleotide substitution and an estimated Gamma shape parameter. The alignment contained 188 taxa, including 33 of our own patient sequences, with an length of 977(2250–3226 relative to HXB2). Two different methods of tree inference were used: a Maximum Likelihood (A) and a Bayesian approach (B). The Maximum Likelihood tree topology was inferred in PhyML v 3.0 with 1000 bootstrap replicates. The Bayesian tree topology was inferred in MrBayes v 2.0 with a total of 10 million steps in the Markov Chain and four independent runs. Inferred trees were visually inspected in FigTree v 1.3.1. The most relavent bootstrap or posterior support values are indicated on the tree topology.