FIG. 2.

HIV-1 subtype classification of RT, protease, and IN regions. (A) The bar graph (right) and phylogenetic tree (left) describe the HIV subtype classification of the IN gene (percentages) of ART-naive patients, FF, SF and RF. (B) The bar graph (right) and phylogenetic tree (left) of HIV subtype classification of RT, and PR regions of N, FF, SF, and RF. Subtype descriptions are embedded in the figure. An in-house Python script was used to label tips with subtype classifications from SCUEAL. A maximum likelihood phylogenetic tree was reconstructed from the alignment using PHYML v20160207 with the default parametric bootstrap estimation of branch supports given the data. The tree was visualized and manually annotated in FigTree (available at: http://tree.bio.ed.ac.uk/software/figtree) and Archaeopteryx v0.9920 beta. IN, integrase. Color images available online at www.liebertpub.com/aid