KaKs_Calculator 2.0:A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies  

作　　者：Dapeng Wang Yubin Zhang Zhang Zhang Jiang Zhu Jun Yu 

机构地区：[1]AS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China [2]Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China [3]Graduate University of Chinese Academy of Sciences, Beijing 100049, China [4]Plant Stress Genomics Research Center, Division of Chemical and Life Sciences & Engineering, King Abdullah University of Science and Technology, Thuwa123955-6900, Saudi Arabia.

出　　处：《Genomics, Proteomics & Bioinformatics》2010年第1期77-80,共4页基因组蛋白质组与生物信息学报（英文版）

基　　金：funded by the National Basic Research Program of China (973 Program) to JY (Grant No.2006CB910404)

摘　　要：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 y-NG, y-LWL, ）,-MLWL, y-LPB, y-MLPB, y-YN and y-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/.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 y-NG, y-LWL, ）,-MLWL, y-LPB, y-MLPB, y-YN and y-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/.

关 键 词：Ka/Ks gamma-series methods sliding window positively selected sites 

分 类 号：TP317.4[自动化与计算机技术—计算机软件与理论] TU228[自动化与计算机技术—计算机科学与技术]