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MKado: a toolkit for McDonald-Kreitman tests of natural selection
Angel G Rivera-Colón1, Clara T Rehmann1, Andrew D Kern1
1Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, OR 97403, United States.
Abstract:
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.
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