PolyPhen (Polymorphism Phenotyping) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.
FATHMM (Functional Analysis through Hidden Markov Models) is a high-throughput web-server capable of predicting the functional, molecular and phenotypic consequences of protein missense variants using hidden Markov models (HMMs) representing the alignment of homologous sequences and conserved protein domains.
FATHMM-MKL , a MKL-based algorithm, capable of predicting the effects of both coding and non-coding variants using nucleotide-based HMM