Software package for predicting deleterious single nucleotide variants using sequence conservation across a phylogenetic sample.
BAD_Mutations (BLAST-Aligned-Deleterious?) performs a likelihood ratio tset (LRT) for the prediction of deleterious single nucleotide variants, as described in Chun and Fay (2009). This approach uses locus-specific synonymous and nonsynonymous substitution rates, so it is only applicable to protein coding regions.
If you use BAD_Mutations in your research, please cite the following:
Kono, T.J., Lei, L., Shih, C.H., Hoffman, P.J., Morrell, P.L. and Fay, J.C., 2018. Comparative genomics approaches accurately predict deleterious variants in plants. G3: Genes, Genomes, Genetics, 8(10), pp.3321-3329. https://doi.org/10.1534/g3.118.200563
Please see our installation guide for help with installation of BAD_Mutations and its dependencies.
For usage instructions and example command lines, please see our Wiki and user manual.