Frequent Toggling between Alternative Amino Acids Is Driven by Selection in HIV-1
Tree branches are coloured according to the codon category of the node at the right end of the branch for sites detected to be (A) diversifying selection or (B) toggling, and (C) a previously identified HLA-associated polymorphism in gag (TW10). Potential escape and reversion mutations are mapped as red and green arrows, respectively. P, likelihood ratio test statistic p-value; D, diversifying selection model; T, toggling model. Both env and gag trees are rooted on HIV-1 subtype B.