HIV-1 Subtypes B and C Unique Recombinant Forms (URFs) and Transmitted Drug Resistance Identified in the Western Cape Province, South Africa
Figure 7
Subtyping analysis of PM003-08 using jpHMM and manual phylogenetic analysis.
A). jpHMM result: A breakpoint is located at position 2594+/−49 (HXB2 numbering). B). Posterior probabilities of the subtypes at each sequence position (original sequence positions) calculated by jpHMM. Posterior probability values are indicated on the y axis and nucleotide positions in the alignment are shown on the x axis. C) and D). Phylogenetic analysis (NJ trees) of two fragments identified by the jpHMM breakpoint. C is a NJ tree of the unclassified fragment whose subtype classification was unresolved by posterior probability analysis and clustered with none of the HIV-1 reference subtypes from the Los Alamos HIV Sequence Database. D is a NJ tree of the subtype C region. Scale corresponds to nucleotide substitutions per site.