SNPdryad is a novel prediction algorithm which only includes protein orthologs in building a multiple sequence alignment.SNPdryad uses different conservation scoring schemes and uses Random Forest as a classifier.
The Zhang Lab, University of Toronto
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SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences.
Wong KC, Zhang Z.
Bioinformatics. 2014 Jan 21.