Open Discovery

Documentation

Discovery 2 is built on Fedora 11, for fedora documentation refer to http://docs.fedoraproject.org

Documentation to the bioinformatics tools

Sequence analysis:

EMBOSS :- http://emboss.sourceforge.net

ClustalX :- http://www.clustal.org

Sequence Manipulation Suite(SMS2):-  http://www.bioinformatics.org/sms2

Phylip :- http://cmgm.stanford.edu/phylip

HMMER :- http://hmmer.janelia.org

Visualization tools

Avogadro (powerful molecular editor):- http://avogadro.openmolecules.net/wiki/Main_Page

Pymol :-  http://pymol.sourceforge.net

SwissPdb Viewer :-http://spdbv.vital-it.ch

Homology Modeling:

Modeller:- http://salilab.org/modeller/

Jackal :- http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Jackal_General_Description

Swiss model(SwissPdbViewer):- http://swissmodel.expasy.org/SWISS-MODEL.html

Molecular Dynamics:

Gromacs:- http://www.gromacs.org

Docking

AutoDock:- http://autodock.scripps.edu

Other tools:

Open Babel – for chemical file format interchanges. :- http://openbabel.org

Chemtool:- for Chemical molecular visualization

Compilers

C

C++

PERL

PYTHON

PYTHON-BIOPYTHON

Due to licensing some of tools are not included in the distribution, You can download at one time and use them on Discovery 2 ,