FIG 3.

Conventional dN/dS tests do not detect positive selection in T-cell epitopes. State-of-the-art methods for detecting positive selection fail to find any enrichment in sites with a dN/dS ratio of >1 at epitopes. (A and B) Percentages of sites estimated to have a dN/dS ratio of >1 by using the hierarchical Bayesian approach implemented in FUBAR (A) and the maximum likelihood approach implemented in FEL (B). (C) Percentages of sites for which FUBAR reports a posterior probability of >0.95 that the dN/dS ratio is >1. (D) Percentages of sites for which FEL reports a dN/dS ratio of >1 with a P value of <0.05.