Fig. 3.—

Example analysis of a gene family using Longest and PALO. The example shown is ENSEMBL gene ENSG00000003096 (brain Kelch-like protein 13), associated with 66 possible protein isoform combinations in 1:1 orthologs from human, mouse, horse, and cow. The first 70 positions of the alignments using the Longest (above) and PALO (below) methods are shown. Longest selects a human protein isoform that shows an extension at the N-terminus. Misalignment of this region results in inflated dN/dS values at the level of the whole protein and an artifactual signal of positive selection (PS) in the human branch.