KaKsCalculator 3. 0: Calculating Selective Pressure on Coding and Non-Coding Sequences

Abstract KaKsCalculator 3. 0 is an updated toolkit that is capable of 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 the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences. As testified on empirical data, KaKsCalculator 3. 0 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 a whole-genome scale. The package of KaKsCalculator 3. 0 is freely available for academic use only at https: //ngdc. cncb. ac. cn/biocode/tools/BT000001.