KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging
- Author:
Zhang ZHANG
1
;
Li JUN
;
Zhao XIAO-QIAN
;
Wang JUN
;
Wong Ka-Shu GANE
;
Yu JUN
Author Information
1. 中国科学院计算技术研究所
- Keywords:
model selection;
model averaging;
AIC;
approximate method;
maximum likelihood method
- From:
Genomics, Proteomics & Bioinformatics
2006;4(4):259-263
- CountryChina
- Language:Chinese
-
Abstract:
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.
