Signals of selection from test set 2 removed by our filtering. Two genes, where strong signals of selection from test set 2, disappear in our reanalysis. For both of these genes, the chimpanzee-specific divergent sites in the alignments of test set 2 are adjacent to a break in the genomic alignments (Rhesus Macaque Genome Sequencing and Analysis Consortium 2007). In our filtering, we remove nucleotides within five positions of the end of a genomic alignment, which appears to abolish these signals. Table 2 shows that 80% of nonsynonymous chimpanzee-specific divergent sites that are present in test set 2, but not our reanalysis, are screened out by our bioinformatic procedure because they are close to the ends of alignments. There are 13 lines in each meta-alignment. Lines 1–7 are as described in Figure 3, but for test set 2. An asterisk indicates that the position is filtered. Macaque divergent sites are not highlighted.
