Fisher's exact test uses estimates of the number of synonymous sites (S), the number of nonsynonymous sites (N), the number of synonymous differences (Sd), and the number of nonsynonymous differences (Nd). It fails for a number of reasons. If the numbers are very large, some mathematical functions may not be able to handle them, although we have tried to avoid this by using logarithms of factorials. To diagnose the problem, compute S, N, Sd, and Nd using the Distances|Pairwise option four times. If you still cannot find the problem, please contact us