ML phylogenetic tree of HIV-1 protease and reverse transcriptase sequences of the <i>pol</i> gene from 45 subjects.

<p>The ML was constructed by PhyML 3.0.1 and visualized in FigTree. The tree is rooted with the HIV-1 group N consensus sequence as an outgroup. 488 non-recombinant <i>pol</i> sequences generated from the 45 subjects were analyzed with HIV-1 reference subtypes from the Los Alamos HIV-1 Sequence Database. HIV-1 inter-subtype recombinant <i>pol</i> DNA sequences were excluded in this figure. HIV-1 reference subtypes A1, C, and D are shown in red, pink and blue, respectively. The other references are shown in orange. Approximate likelihood ratio test (aLRT) values of ≥0.95 were considered significant and are shown by an asterisk (*). The scale at the bottom of the figure corresponds to 0.01 nucleotide substitutions per site.