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Figure 2 | Retrovirology

Figure 2

From: Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants

Figure 2

Trees generated for phylogenetic cluster analysis. Phylogenetics cluster analysis was carried out using day 63 viral sequences from P1 and P2. Zoomed-in images of trees are shown in Figure 2 for the env fragment in a. and b., the gag fragment in c. and d., and the pol fragment in e. and f.. Results from two different methods of cluster analysis are shown for each fragment: ML (PhyML) trees in a., c., and e., and Bayesian MCMC based consensus trees in b., d., and f.. Terminal nodes represent sequences sampled from P1 (blue circles) or P2 (red circles), as well as reference sequences. Env sequences for P1 and P2 were sampled by SGA and represent gap-stripped alignments 1305 nucleotides in length. Gag and pol fragments were sampled by bacterial cloning. The full tree images can be viewed in Additional Figures 1 and 2. All scale bars show 0.05, equivalent to 5% divergence. ML bootstrap values or Bayesian MCMC based posterior probabilities for the clustering of P1 and P2 are given as percentages next to the common ancestor node.

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