KaKs_Calculator adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting 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 KaKs_Calculator.
https://code.google.com/p/kaks-calculator/
计算kaks值的软件，GY model 算的很慢。
下在exe的要需要代理。