PolyPhen-2 is a new development of the PolyPhen tool for annotating coding nonsynonymous SNPs. Some of the highlights of the new version are:

• High quality multiple sequence alignment pipeline
• Probabilistic classifier based on machine-learning method
• Optimized for high-throughput analysis of the next-generation sequencing data

• Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010). PubMed PDF Supplemental Information

1. Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet, Chapter 7:Unit7.20 (2013). PubMed PDF
2. Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30(17):3894-3900 (2002). PubMed PDF
3. Sunyaev SR, Eisenhaber F, Rodchenkov IV, Eisenhaber B, Tumanyan VG, Kuznetsov EN. PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng 12(5):387-394 (1999). PubMed PDF