KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences

Abstract

KaKs_Calculator 3.0 is an updated toolkit that is capable for calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as non-coding nucleotide substitution rate normalized by synonymous substitution rate of adjacent coding sequences. As testified on empirical data, it shows effectiveness to detect the strength and mode of selection operated on molecular sequences, accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at whole genome scale. The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.