Figure 2

SplitsTree analysis of the HIV-1 Bolivian BF1 pol regions. The splits graph was constructed using NeighborNet methodology with pairwise distance input, which was estimated by F84 distance. The scale bar indicates 10% nucleotide sequence divergence. Reference sequences were indicated by subtype letter or CRF number. The alignment was prepared with HIV-1 group M subtypes B and F1 and CRF_BFs from South America. Four clusters containing studied samples were detected and are indicated with a circle. Representative bootscanning plots were generated for each cluster. Bootscan analysis was performed on a sliding window of 200 nt of the query sequences moving along an alignment of reference sequences by increments of 20 nt. Reference samples used for these analyses are discriminated in the figure legend.