Optional Add-ons
================

These are the specialist analysis software packages and data sources that add power to Polyphony. It is very much the philosophy of this project to combine pre-existing, open source, published tools where possible.

**Optional python modules**

-  `E.T.E. <http://ete.cgenomics.org/>`_, for nice interactive tree diagrams

**Optional programs**

-  `NCONT <http://www.ccp4.ac.uk/html/ncont.html>`_ from `CCP4 <http://www.ccp4.ac.uk/>`_, for crystal contact calculation. Requires a license but is free for academics
-  `fpocket <http://fpocket.sourceforge.net/>`_, for pocket calculations, including druggability prediction
-  `Jalview <http://www.jalview.org/>`_, for multiple sequence alignment annotation

**Optional database access**

-  The Credo database of intermolecular interactions is currently undergoing a major revision. Web access will hopefully be available soon (21/12/12). Watch for updates in `Adrian Schreyer's blog <http://blog.adrianschreyer.eu/>`_.
-  The `Piccolo <http://www-cryst.bioc.cam.ac.uk/~richard/piccolo/piccolo.php>`_ database of protein-protein interatomic interactions is available for download. Code is included for accessing it using `sqlalchemy <http://www.sqlalchemy.org/>`_.