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. 2014 Sep 9;9(9):e107349. doi: 10.1371/journal.pone.0107349

Figure 3. Recombination and phylogenetic reanalysis of CRF24_BG and CRF44_BF.

Figure 3

(A) Results of CRF24 from both jpHMM and RDP3 indicate there is a whole B segment in the pol region rather than three separate segments in the previous structure. The result was further confirmed by the phylogenetic tree. The position spans 2588–4153 is shown above the tree. The tree was constructed using PhyML program implemented in the RDP3 software package. Bootstrap replications of ≥350 (i.e., bootstrap support values of ≥70%) are considered to be significant. The very small part of the B segment (8697–8750) in env was not detected by either newly-used program. (B) Both jpHMM and RDP3 indicate that in CRF44, there is a whole B segment in the pol region rather than two separate segments in previous mosaic structure. The result was further confirmed by the phylogenetic analysis. The position spans 2470–3705 is shown above the tree. The tree was constructed using PhyML program implemented in the RDP3 software package. Bootstrap replications of ≥350 (i.e., bootstrap support values of ≥70%) are considered to be significant. A very small part of B segment (6342–6446) in env was not detected by either new program.