KaKs Calculator is a program package for Windows that allows you to calculate nonsynonymous and synonymous substitution rates using model selection and averaging. The software solution implements a set of candidate simulations in a maximum likelihood framework. Moreover, it adapts the Akaike criterion to measure fitness between models and source data.

Detailed information

The calculator provides comprehensive information estimated from compared sequences, including the number of Ka and Ks sites and substitutions, GC contents, maximum likelihood scores, as well as AICC. In addition, the application incorporates several other methods, and gives you the ability to run one or more to run at a time. If you want to perform a wide range of mathematical calculations, you may try another utility called Calc98.

Modes of operation

The approximate method consists of three basic steps. The first is for counting the numbers of synonymous and nonsynonymous sites, while the second is reserved for doing the same with substitutions. The last is for correction. The maximum likelihood method relies on the probability theory to finish the aforementioned steps in one go.

Features

free to download and use;
compatible with modern Windows versions;
gives you the ability to calculate substitution rates;
you can run multiple methods at the same time;
the program may be launched from a USB drive;
it is possible to specify the genetic code.