Figure 2

An exploratory ML tree calculated from fragments between breakpoints of sequences identified in this study (indicated by black circles), published sequences with identical breakpoints (indicated by triangle) and reference sequences of subtype A-D, F-H, J and K http://hiv-web.lanl.gov. (A) Tree of the viral genomes corresponding to the subclade F1 segments (HXB2 nucleotides 623-9347). (B) Tree of the viral genomes corresponding to the subtype B segments in the LTR region (HXB2 nucleotides 9348-9719). For clarity purposes, the tree was midpoint rooted. The approximate likelihood ratio test (aLRT) values of ≥ 90% are indicated at nodes. The scale bar represents 0.05 nucleotide substitution per site.