KaKs.Calculator is a software package designed to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging. The software aims to provide accurate evolutionary information by integrating a set of candidate models in a maximum likelihood framework and using the Akaike information criterion (AIC) to measure the fitness between models and data. The package includes various substitution models, ranging from the Jukes-Cantor (JC) model to the general time-reversible (GTR) model, and incorporates several existing methods for calculating Ka and Ks. The software is freely available for academic use and can be run on Unix/Linux, Windows, and other operating systems. It provides comprehensive information such as the number of synonymous and nonsynonymous sites and substitutions, GC contents, maximum likelihood scores, and AIC_C. KaKs.Calculator is particularly useful for in-depth studies on phylogeny and molecular evolution, offering more reliable evolutionary information compared to other existing tools.KaKs.Calculator is a software package designed to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging. The software aims to provide accurate evolutionary information by integrating a set of candidate models in a maximum likelihood framework and using the Akaike information criterion (AIC) to measure the fitness between models and data. The package includes various substitution models, ranging from the Jukes-Cantor (JC) model to the general time-reversible (GTR) model, and incorporates several existing methods for calculating Ka and Ks. The software is freely available for academic use and can be run on Unix/Linux, Windows, and other operating systems. It provides comprehensive information such as the number of synonymous and nonsynonymous sites and substitutions, GC contents, maximum likelihood scores, and AIC_C. KaKs.Calculator is particularly useful for in-depth studies on phylogeny and molecular evolution, offering more reliable evolutionary information compared to other existing tools.