Table 1.

Number of genes inferred to have a positively selected site(s). Inference is based on PAML models M7 and M8 (a and b), models M1a and M2a (c and d), and models M7 and M8 after removing gaps (e and f) for 12 species alignments generated with each of the six aligners; and models M7 and M8 for melanogaster group alignments (g and h)

“Total” indicates the number of genes that were in at least one of the aligners' counts; numbers in brackets in g and h indicate the number of genes if the “masked” instead of unmasked T-Coffee alignments are used. The significance cutoffs (95% and 99% posterior probability) are indicated on the second row.