title: KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies.
abstract: We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including gamma-NG, gamma-LWL, gamma-MLWL, gamma-LPB, gamma-MLPB, gamma-YN and gamma-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5' to 3' direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C++ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https://sourceforge.net/projects/kakscalculator2/.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.
authors.forename: Dapeng
authors.initials: D
authors.lastname: Wang
authors.forename: Yubin
authors.initials: Y
authors.lastname: Zhang
authors.forename: Zhang
authors.initials: Z
authors.lastname: Zhang
authors.forename: Jiang
authors.initials: J
authors.lastname: Zhu
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D000818:Animals; D005075:Biological Evolution; D003201:Computers; D006801:Humans; D012984:Software; D012985:Software Design
references.citation: Nat Genet. 2001 May;28(1):58-63
references.pmid: 11326277
references.citation: Bioinformatics. 2004 Nov 1;20(16):2867-8
references.pmid: 15130925
references.citation: Genomics Proteomics Bioinformatics. 2006 Nov;4(4):259-63
references.pmid: 17531802
references.citation: Genomics Proteomics Bioinformatics. 2006 Aug;4(3):173-81
references.pmid: 17127215
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: Bioinformatics. 2005 Mar 1;21(5):676-9
references.pmid: 15509596
references.citation: Bioinformatics. 2009 Jun 1;25(11):1451-2
references.pmid: 19346325
references.citation: Biol Direct. 2009 Jun 16;4:20
references.pmid: 19531225
references.citation: J Mol Evol. 2009 Apr;68(4):414-23
references.pmid: 19308632
references.citation: Mol Biol Evol. 2007 Aug;24(8):1586-91
references.pmid: 17483113
references.citation: Mol Biol Evol. 2004 May;21(5):819-27
references.pmid: 14963090
references.citation: BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S13
references.pmid: 19091012
references.citation: Genome Res. 2002 Oct;12(10):1611-8
references.pmid: 12368254
references.citation: Genomics Proteomics Bioinformatics. 2009 Sep;7(3):116-27
references.pmid: 19944384