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

Assemblers and related software

• Software/Cap3
• Software/Mira
• Software/Oases
• Software/Velvet
• Software/Tablet
• Software/Trinity
• Software/FastQc
• Software/Blast2Go
• Software/RocheNewbler

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