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BAD_Mutations

BAD_Mutations predicts deleterious substitutions in protein coding regions using sequence conservation across an alignment. It explicitly uses local substitution rates to test the hypothesis that a nonsynonymous variant is deleterious.

The model that BAD_Mutations uses was developed by Chun and Fay 2009. It was first applied to plant genomes by Kono et al. 2016.

If you use BAD_Mutations, please cite the software publication (Kono et al. 2018). This publication also includes a survey of known phenotype-altering variants in Arabidopsis thaliana.

Latest Version

The latest stable release of BAD_Mutations is 1.0.

For the latest changes to the code, clone the GitHub repository. For the latest untested changes, check out the dev branch.

Usage Guide

For a quick refresher on BAD_Mutations usage, please see the quickstart guide. For an exhaustive explanation, see the manual.