Table of Contents


Downloadable material.



The software provided herein is free for academic instruction and research use only. Commercial licenses are available to legal entities, including companies and organizations (both for-profit and non-profit), requiring the software for general commercial use. To obtain a commercial license please, contact us via e-mail.


This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. The code should not be modified and/or redistributed without the permission of the authors.

Item File(s)
PolyPhen-2 standalone source code, see INSTALL
file included for installation instructions


Item File(s)
PolyPhen-2 bundled databases (3.7G) polyphen-2.2.2-databases-2011_12.tar.bz2
Precomputed MLC protein alignments (2.4G) polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2
Precomputed MultiZ genomic alignments (1.8G) polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
MD5 checksums for all tarballs md5sum.txt


Item File(s)
HumDiv & HumVar training sets README
Whole human exome sequence space annotations README


Item Description File(s)
Nat Methods 7, 248-9 (2010) PolyPhen-2 paper PDF Supplement
Nucleic Acids Res 30, 3894-900 (2002) PolyPhen paper PDF
Protein Eng 12, 387-94 (1999) PSIC paper PDF