PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.

• Latest version: 2.2.2
• Added: March, 2017
• Link: http://genetics.bwh.harvard.edu/pph2/dokuwiki/start

See versions of polyphen which are available:

$ module avail polyphen

Load polyphen:

$ module load polyphen

Notes from the sysadmin during installation:

$ cd /tmp
$ wget -qO- http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.2.2r405c.tar.gz | tar xzv
$ cd polyphen-2.2.2/
$ scl enable devtoolset-3 bash
$ module load perl/5.22.3
$ cpanm DBD::SQLite
$ sudo mkdir -p /export/apps/polyphen/2.2.2
$ sudo chown -R joguya:joguya /export/apps/polyphen/2.2.2
$ ./configure
$ make download
$ make
$ make install
$ cp -r . /export/apps/polyphen/2.2.2
$ sudo chown -R root:root /export/apps/polyphen/2.2.2