Codons under positive selection in the PML sample.

VP1 sequences isolated from PML patients and random subsets of sequences isolated from healthy subjects were further analyzed using PAML [23]. We examined multiple models of sequence evolution incorporated in PAML including purely neutral model (M0), nearly neutral model (M1), model with positive selection (M2) and additional more complex models (M3�CM8). We used likelihood ratio test (LRT) to compare the difference between models M1 and M2 to test for positive selection. P-values for positive selection in three datasets are shown together with Bayesian posterior probabilities for each codon position. Residues with Bayes Empirical Bayes posterior probabilities exceeding 0.5 are shown.