HLA allele associated polymorphisms [4] at detected toggling sites.

#sites without HLA associated polymorphisms.*sites detected with diversifying selection model (D); WT, wild type states are amino acids for which there is a significant difference between null and alternate models in a likelihood ratio test (boldface indicates state with largest log likelihood); E, escape; R, reversion; tc, proportion of time spent in class c (Figure 1) for wild type state with the largest likelihood.