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