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| KaKs_Calculator： Calculating Ka and Ks Through Model Selection and Model Averaging | |
| 引用本文： | Zhang Z,Li J,Zhao XQ,Wang J,Wong GK,Yu J. KaKs_Calculator： Calculating Ka and Ks Through Model Selection and Model Averaging[J]. 基因组蛋白质组与生物信息学报(英文版), 2006, 4(4): 259-263. DOI: 10.1016/S1672-0229(07)60007-2 |
| 作者姓名： | Zhang Z Li J Zhao XQ Wang J Wong GK Yu J |
| 作者单位： | [1]Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China [2]Beijing Instituteof Genomics, Chinese Academy of Sciences, Beijing 101300, China [3]Graduate School of Chinese Academyof Sciences, Beijing 100049, China [4]James D. Watson Institute of Genome Sciences, Zhejiang University,Hangzhou 310007, China [5]UW Genome Center, University of Washington, Seattle, WA 98195, USA |
| 基金项目： | 清华大学校科研和教改项目;国家自然科学基金 |
| 摘 要： | KaKs_Calculator is a software package that calculates nonsynonymous （Ka） and synonymous （Ks） substitution rates through model selection and model averaging. Since existing methods for this estimation adopt their specific mutation （substitution） models that consider different evolutionary features, leading to diverse estimates, KaKs_Calculator implements a set of candidate models in a maximum likelihood framework and adopts the Akaike information criterion to measure fitness between models and data, aiming to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into this software. KaKs_Calculator, including source codes, compiled executables, and documentation, is freely available for academic use at http：//evolution.genomics.org.cn/software.htm. |
| 关 键 词： | KaKs替换比计算器 软件包 模型选择 模型平衡 AIC 逼近法 最大似然法 |
KaKs_Calculator: calculating Ka and Ks through model selection and model averaging |
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| Zhang Zhang,Li Jun,Zhao Xiao-Qian,Wang Jun,Wong Gane Ka-Shu,Yu Jun. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging[J]. Genomics, proteomics & bioinformatics, 2006, 4(4): 259-263. DOI: 10.1016/S1672-0229(07)60007-2 | |
| Authors: | Zhang Zhang Li Jun Zhao Xiao-Qian Wang Jun Wong Gane Ka-Shu Yu Jun |
| Affiliation: | aInstitute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China bBeijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China cGraduate School of Chinese Academy of Sciences, Beijing 100049, China dJames D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310007, China eUW Genome Center, University of Washington, Seattle, WA 98195, USA |
| Abstract: | KaKs_Calculator is a software package that calculates nonsynonymous(Ka) andsynonymous(Ks) substitution rates through model selection and model averag-ing.Since existing methods for this estimation adopt their specific mutation(substitution) models that consider different evolutionary features,leading todiverse estimates,KaKs Calculator implements a set of candidate models in amaximum likelihood framework and adopts the Akaike information criterion tomeasure fitness between models and data,aiming to include as many featuresas needed for accurately capturing evolutionary information in protein-coding se-quences.In addition,several existing methods for calculating Ka and Ks arealso incorporated into this software.KaKs Calculator,including source codes,compiled executables,and documentation,is freely available for academic use athttp://evolution.genomics.org.cn/software.htm. |
| Keywords: | model selection model averaging AIC approximate method maximum likelihood method |
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