Zhang Zhang, Li Jun, Zhao Xiao-Qian, Wang Jun, Wong Gane Ka-Shu, Yu Jun
Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China.
Genomics Proteomics Bioinformatics. 2006 Nov;4(4):259-63. doi: 10.1016/S1672-0229(07)60007-2.
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是一个软件包，它通过模型选择和模型平均来计算非同义（Ka）和同义（Ks）替换率。由于现有的这种估计方法采用了考虑不同进化特征的特定突变（替换）模型，导致估计结果各不相同，KaKs_Calculator在最大似然框架中实现了一组候选模型，并采用赤池信息准则来衡量模型与数据之间的拟合度，旨在纳入尽可能多的特征，以便准确捕捉蛋白质编码序列中的进化信息。此外，该软件还纳入了几种现有的计算Ka和Ks的方法。
