KaKs_Calculator 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, KaKs_Calculator 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 KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.
Mol Biol Evol. 1994 Sep;11(5):725-36
[PMID:
7968486]
Mol Biol Evol. 1993 Mar;10(2):271-81
[PMID:
8487630]
Mol Biol Evol. 2013 Apr;30(4):772-80
[PMID:
23329690]
BMC Evol Biol. 2008 Jan 23;8:17
[PMID:
18215302]
Science. 2004 May 28;304(5675):1321-5
[PMID:
15131266]
Genomics Proteomics Bioinformatics. 2006 Aug;4(3):173-81
[PMID:
17127215]
Biochem Biophys Res Commun. 2012 Mar 23;419(4):779-81
[PMID:
22390928]
Brief Bioinform. 2019 Sep 27;20(5):1853-1864
[PMID:
30010717]
Trends Genet. 2014 Apr;30(4):121-3
[PMID:
24613441]
Nucleic Acids Res. 2013 Sep;41(17):8220-36
[PMID:
23847102]
Nucleic Acids Res. 2021 Jan 8;49(D1):D1020-D1028
[PMID:
33270901]
RNA Biol. 2017 Dec 2;14(12):1705-1714
[PMID:
28837398]
Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80
[PMID:
20451164]
Annu Rev Genet. 2008;42:287-99
[PMID:
18983258]
J Mol Evol. 1985;22(2):160-74
[PMID:
3934395]
Br J Cancer. 2016 Jun 14;114(12):1395-404
[PMID:
27172249]
Nucleic Acids Res. 2022 Jan 7;50(D1):D190-D195
[PMID:
34751395]
J Mol Evol. 2009 Apr;68(4):414-23
[PMID:
19308632]
Mol Biol Evol. 2000 Jan;17(1):32-43
[PMID:
10666704]
Nucleic Acids Res. 2022 Jan 7;50(D1):D27-D38
[PMID:
34718731]
Nucleic Acids Res. 2019 Jan 8;47(D1):D128-D134
[PMID:
30329098]
Trends Genet. 2002 Sep;18(9):486
[PMID:
12175810]
Genomics Proteomics Bioinformatics. 2021 Jun;19(3):377-393
[PMID:
34284134]
Methods Mol Biol. 2012;856:141-59
[PMID:
22399458]
Mol Biol Evol. 1985 Mar;2(2):150-74
[PMID:
3916709]
BMC Evol Biol. 2011 Apr 16;11:102
[PMID:
21496275]
Mol Biol Evol. 2007 Aug;24(8):1586-91
[PMID:
17483113]
J Mol Evol. 1993 Jan;36(1):96-9
[PMID:
8433381]
Mol Biol Evol. 2010 Jun;27(6):1226-34
[PMID:
20150340]
Nat Rev Cancer. 2018 Jan;18(1):5-18
[PMID:
29170536]
Genetics. 2004 Jun;167(2):949-58
[PMID:
15238543]
Cell Physiol Biochem. 2018;47(3):893-913
[PMID:
29843138]
Genomics Proteomics Bioinformatics. 2021 Aug;19(4):602-610
[PMID:
34536568]
Genomics Proteomics Bioinformatics. 2006 Nov;4(4):259-63
[PMID:
17531802]
Nature. 2012 Sep 6;489(7414):57-74
[PMID:
22955616]
J Mol Med (Berl). 2013 Jul;91(7):791-801
[PMID:
23529762]
Mol Biol Evol. 1986 Sep;3(5):418-26
[PMID:
3444411]
Nucleic Acids Res. 2013 Feb 1;41(4):2073-94
[PMID:
23293005]
Mol Biol Evol. 2004 Dec;21(12):2290-8
[PMID:
15329386]
Nucleic Acids Res. 2000 Mar 1;28(5):1221-7
[PMID:
10666466]
Trends Genet. 1999 Apr;15(4):134-5
[PMID:
10203817]
Nature. 2009 Mar 12;458(7235):223-7
[PMID:
19182780]
OMICS. 2019 Nov;23(11):549-559
[PMID:
31689173]
Nat Rev Genet. 2011 Jan;12(1):32-42
[PMID:
21102527]
Biochem Soc Trans. 2020 Aug 28;48(4):1545-1556
[PMID:
32756901]
BMC Evol Biol. 2006 Jun 02;6:44
[PMID:
16740169]
Mol Biol Evol. 2007 Feb;24(2):522-31
[PMID:
17122369]
