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. 2012 Nov 1;206(9):1433–1442. doi: 10.1093/infdis/jis503

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Published by Oxford University Press on behalf of the Infectious Diseases Society of America 2012.

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Figure 3. — Maximum composite likelihood Neighbor-joining phylogenetic trees of gp41 viral consensus sequences (containing >0.5% of total sequence reads) from 3 transmitting couples derived from deep 454 next-generation sequencing of recipient strains (blue), donor early strains (green), and donor transmission strains (red) are shown. The closest or transmitted strain (TS) to the recipient viral population is indicated by an arrow and is either closely related to sequences found in the donor near the time of transmission only (A), in the donor's earlier sample only (B), or both (C). The number of repeated read sequences represented by each consensus sequence is shown at the end of the consensus identifier. Bootstrap values (500 replicates) >80% are shown. Distance is indicated for each individual tree, and samples are grouped with a selection of subtype reference sequences and random sequences from individuals in Rakai (black).

Figure 3. — Maximum composite likelihood Neighbor-joining phylogenetic trees of gp41 viral consensus sequences (containing >0.5% of total sequence reads) from 3 transmitting couples derived from deep 454 next-generation sequencing of recipient strains (blue), donor early strains (green), and donor transmission strains (red) are shown. The closest or transmitted strain (TS) to the recipient viral population is indicated by an arrow and is either closely related to sequences found in the donor near the time of transmission only (A), in the donor's earlier sample only (B), or both (C). The number of repeated read sequences represented by each consensus sequence is shown at the end of the consensus identifier. Bootstrap values (500 replicates) >80% are shown. Distance is indicated for each individual tree, and samples are grouped with a selection of subtype reference sequences and random sequences from individuals in Rakai (black).