Phylogenetic analysis of HIV-1 gag sequences. NJ tree of HIV-1 gag nucleotide fragments obtained from blood and seminal plasma collected in 2001–2005. Distances were calculated with the Tamura-Nei method using the gamma model with α = 0.25, and 1000 bootstrap replicated were analysed. The three separate clusters comprised of strains B1, B2, and CRF01_AE are indicated. A representative sequence set was used to draw the phylogenetic tree.