Example of different alignment between test set 1 and our analysis (TEC). Different alignments between the analysis of test set 1 and our reanalysis are one of the largest contributors to the signal of chimpanzee-specific PSGs, accounting for 30% of codons with at least two chimpanzee-specific changes. By visual inspection of the alignments where these problems occur, we concluded that a major problem appears to be missing sequence in the input data used in the published study. This example shows the TEC gene, where the alignment based on the panTro1 4× assembly (prefixed by ENSPTRP) gives a strong signal of positive selection. However, our reanalysis (shown in lines “human_dna,” “chimp_dna,” and “macaque_dna”) show that there is an alignment solution without evidence for positive selection. A description of each line is given in the legend for Figure 3.
