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dc.contributor.authorWang, Dapeng
dc.contributor.authorZhang, Yubin
dc.contributor.authorZhang, Zhang
dc.contributor.authorZhu, Jiang
dc.contributor.authorYu, Jun
dc.date.accessioned2015-05-10T14:28:23Z
dc.date.available2015-05-10T14:28:23Z
dc.date.issued2010-05-06
dc.identifier.citationKaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies 2010, 8 (1):77 Genomics, Proteomics & Bioinformatics
dc.identifier.issn16720229
dc.identifier.doi10.1016/S1672-0229(10)60008-3
dc.identifier.urihttp://hdl.handle.net/10754/552548
dc.description.abstractWe 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 γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, γ-YN and γ-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/.
dc.publisherElsevier BV
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S1672022910600083
dc.rightsArchived with thanks to Genomics, Proteomics & Bioinformatics. http://creativecommons.org/licenses/by-nc-sa/3.0/
dc.subjectKa/Ks
dc.subjectgamma-series methods
dc.subjectsliding window
dc.subjectpositively selected sites
dc.titleKaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
dc.typeArticle
dc.contributor.departmentBiological and Environmental Science and Engineering (BESE) Division
dc.contributor.departmentCenter for Desert Agriculture
dc.contributor.departmentPlant Stress Genomics Research Lab
dc.identifier.journalGenomics, Proteomics & Bioinformatics
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionCAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
dc.contributor.institutionInstitute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
dc.contributor.institutionGraduate University of Chinese Academy of Sciences, Beijing 100049, China
kaust.personZhang, Zhang
refterms.dateFOA2018-06-14T07:35:34Z
dc.date.published-online2010-05-06
dc.date.published-print2010-03


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