Figure 2 | Scientific Reports

Figure 2

From: Near full-length HIV-1 subtype B sequences from the early South African epidemic, detecting a BD unique recombinant form (URF) from a sample in 1985

Figure 2

Subtyping analyses of the unique recombinant form (URF) of R605, a BD recombinant sequence according to jumping profile Hidden Markov Model (jpHMM), LANL and phylogenetic analyses. Phylogenetic analyses (ML tree) according to breakpoint located at position (862–3918 bp) in the gag - pol region clusters amongst subtype B sequences. ML tree according to breakpoint position (3918–5974 bp) in the pol – vif region clusters amongst subtype D sequences. ML tree according to breakpoint position (5974–9187 bp) in the vpu – env region clusters amongst subtype B sequences. In order to validate the sequences a total of 100 bootstrap replicates was carried to infer a ML phylogenetic tree.

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