== 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 2GB. === Statistics * [[Software/R]] - The R language för statistical computing (Versions: 3.6.0) === Python * [[Software/Python]] * [[Software/NumPy]] * [[Software/BioPython]] == Old software list == Software below might work after loading the module legacy. === 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