Detecting accelerated exon evolution. Genomic regions containing transcripts are extracted from a masked genome. Whole-genome shotgun (WGS) reads of one or more species are aligned against these regions. All alignments are summarized within a composite sequence that records all high-quality differences present in at least two alignments. Rates of differences per nucleotide within exons and neighboring introns are computed, and a likelihood-ratio test is applied.
Lorente-Galdos et al. Genome Biology 2013 14:R9 doi:10.1186/gb-2013-14-1-r9