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

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© 2014 Jia et al

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) Genome maps of CRF07_BC from different sources. The top picture shows the original mosaic structure from the Los Alamos HIV database. The middle image is the jpHMM-derived mosaic structure. The bottom image is the RDP3-derived mosaic structure. The standard representatives are marked by different colors, as indicated. (B) Phylogenetic relationship of the region spanning HXB2 nt 790–2053 in gag with the representatives of the major HIV-1 (group M) subtypes based on a new mosaic structure. The tree was constructed using the Maximum likelihood method implemented in Mega 5. Values at the nodes indicate the percent bootstraps in which the cluster to the right was supported. Bootstrap support values of ≥70% were considered significant. Only bootstraps of 70% and higher are shown. Subtype C clades are identified by brackets. Branch lengths are drawn to scale. Positions are shown beside the tree.