{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T17:03:29Z","timestamp":1781975009861,"version":"3.54.5"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":5184,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"funder":[{"DOI":"10.13039\/501100005222","name":"Jyv\u00e4skyl\u00e4n Yliopisto","doi-asserted-by":"publisher","award":["2006CB910404"],"award-info":[{"award-number":["2006CB910404"]}],"id":[{"id":"10.13039\/501100005222","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 \u03b3-NG, \u03b3-LWL, \u03b3-MLWL, \u03b3-LPB, \u03b3-MLPB, \u03b3-YN and \u03b3-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\u2019 to 3\u2019 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\/.<\/jats:p>","DOI":"10.1016\/s1672-0229(10)60008-3","type":"journal-article","created":{"date-parts":[[2010,5,6]],"date-time":"2010-05-06T10:01:09Z","timestamp":1273140069000},"page":"77-80","source":"Crossref","is-referenced-by-count":1798,"title":["KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies"],"prefix":"10.1093","volume":"8","author":[{"given":"Dapeng","family":"Wang","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yubin","family":"Zhang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Institute of Computing Technology, Chinese Academy of Sciences , Beijing, 100190 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Plant Stress Genomics Research Center, Division of Chemical and Life Sciences & Engineering, King Abdullah University of Science and Technology , Thuwal, 23955-6900 , Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiang","family":"Zhu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Yu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Institute of Computing Technology, Chinese Academy of Sciences , Beijing, 100190 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,5,5]]},"reference":[{"key":"2024051008270018600_bib1","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol. 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