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Figure 3 | Virology Journal

Figure 3

From: HIV-1 diversity in an antiretroviral treatment naïve cohort from Bushbuckridge, Mpumalanga Province, South Africa

Figure 3

Phylogenetic analysis of the partial pol gene, using MEGA 6. The evolutionary history was inferred by using the ML method based on the GTR model. The tree with the highest log likelihood (−9574.7386) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 1.1121)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 45.2893% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 49 nucleotide sequences and included all codon positions. There were a total of 1062 positions in the final dataset.

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