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From input of non-synonymous single nucleotide polymorphism (SNP), this tool uses analysis of multiple sequence alignments and protein stuctures to predict, annotate, and visualize SNP features. PolyPhen-2 is further development of PolyPhen.


Biology, Genetics, DNA polymorphism


  • Operation: Prediction and recognition
  • Software interface: Command-line interface, web user interface
  • Language: C
  • Operating system: Linux, Mac OS X
  • License: Other
  • Cost: Free for academic instruction and research use only. Commercial licenses are available.
  • Version name: 2.2.2
  • Credit: National Institutes of Health Grant R01 GM078598.
  • Contact: Sunyaev SR ssunyaev at
  • Collection: -


Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. "A method and server for predicting damaging missense mutations." Nat Methods. 2010 Apr;7(4):248-9. doi: 10.1038/nmeth0410-248.
PMID: 20354512
PMCID: PMC2855889

Adzhubei I, Jordan DM, Sunyaev SR. "Predicting functional effect of human missense mutations using PolyPhen-2." Curr Protoc Hum Genet. 2013 Jan;Chapter 7:Unit7.20. doi: 10.1002/0471142905.hg0720s76.
PMID: 23315928
PMCID: PMC4480630

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