FIG 2.

Threshold to determine which sites are experiencing diversifying selection. For each HA amino acid site, FUBAR returns the probability that the observed ratio of nonsynonymous to synonymous mutations is greater than the expected ratio. A histogram of the number of amino acid positions (count) for a given range of probabilities is plotted. A conservative threshold of 0.8 was chosen within the minimum range observed between the two major modes in order to reduce the number of false-positive calls.