== Available Software ==
Before any software can be used, the corresponding module has to be loaded. This is done by typing `module load software_name`. You can use `module avail` or `module whatis` to list the names of the available software modules. To list the modules currently loaded, use `module list`

In many cases you will need to submit your jobs to GridEngine. This is the case when the runtime exceeds 30 minutes or the memory requirement exceeds 1GB.

=== Assemblers and related software ===
 * Software/Cap3
 * Software/Mira
 * Software/Oases
 * Software/Velvet
 * Software/Tablet
 * Software/Trinity
 * Software/FastQc
 * [[Software/Blast2Go]]
 * Software/RocheNewbler
 * Software/TopHat
 * Software/CuffLinks
 * 

=== Homology searches and alignment ===
 * Software/NCBIBlast
 * Software/Mafft
 * Software/Mosaik

=== Population Genetics ===
 * Software/MrBayes (not yet installed)
 * [[Software/MigrateN]]

=== Programming languages and libraries ===
 * Perl [http://www.perl.org] modules for BioPerl [http://www.bioperl.org/wiki/Main_Page] - These are useful if you write your own perl scripts.
 * Python [http://www.python.org] modules for BioPython [http://biopython.org/wiki/Biopython] - The Python ditto to BioPerl.
 * Software/OpenMpi - Message Passing Interface