MKado is a Python toolkit for performing McDonald-Kreitman (MK) tests of natural selection from aligned coding sequences. It implements the standard MK test as well as a wide variety of its extensions and related statistics, including a number of methods for estimating the fraction of adaptive substitutions (α) while accounting for slightly deleterious mutations, with a unified command-line interface and Python API. MKado supports parallel batch processing of thousands of genes with near-linear scaling, and provides publication-ready visualizations including volcano plots and asymptotic α curves.
Rivera-Colón et al. (Mon,) studied this question.