== 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.

Please edit the software pages and add notes if you find the information incomplete, or if you want to share any specifics on how the software is used.

=== Statistics
  * [[Software/R]] - The R language för statistical computing (Versions: 3.6.0)
  * [[Software/IQ-TREE]] - Efficient software for phylogenomic inference (Version 1.6.12)

=== Python
  * [[Software/Python]]
  * Software/NumPy
  * Software/BioPython
  * Software/MatPlotLib

=== Sequencing
  * Software/SamTools


== Legacy

The following software and modules used to be available before the grid upgrade. They have not been tested on the new grid, but may work without any issues. If you need to use them. Please try out. To load them, first load the module load the module "legacy", and then the appropriate module. If the software fails, please ask create an issue here in Trac and ask for the software or drop a mail to Les.

{{{
   AEGeAn/0.9.3                   emboss/6.6.0                       openmpi/2.0.3        (D)
   AEGeAn/0.9.4            (D)    exabayes/1.5                       openpyxl/2.2.2
   PBSuite/14.6.24                exonerate/2.2.0                    orthofinder/1.1.8
   R/2.12.0                       fastme/2.1.5                       orthomcl/2.0.8
   R/2.15.1                       fastqc/0.10.1                      p/mykopat-gbrowse
   R/3.0.2                 (D)    fastqc/0.11.5               (D)    paml/4.7
   R/3.2.0                        faststructure/1.0                  parallelfork/1.1
   R/3.4.1                        fastx_toolkit/0.0.13.2             pbh5tools/0.8.0
   abyss/1.3.4                    filespeclink/filespeclink          pear/0.9.10
   abyss/1.3.5_kmer128            flexbar/3.0.3                      perl/5.16.1
   abyss/1.3.5                    frc_align/20130408                 perl/5.16.2          (D)
   abyss/1.3.6_kmer128            freebayes/0.9.6                    phylip/3.695
   abyss/1.3.6             (D)    freebayes/0.9.21                   picardtools/1.107
   amos/3.1.0                     freebayes/1.0.0-19-gefe685d (D)    picardtools/2.10.0   (D)
   antismash/2.0.2                gatk/2.8-1                         pysam/0.7.4
   antismash/3.0.5.1       (D)    gatk/3.7.0                         python/2.7.3
   augustus/2.6.1                 gatk/4.0.5.1                (D)    python3/3.3.2
   augustus/2.7                   gcc/7.1.0                          python3/3.3.3
   augustus/3.0.3          (D)    geneid/1.4.4_110113                pyvcf-py3/0.6.7
   bamm/2.5.0                     genometools/1.5.2                  pyvcf/0.6.3
   bamtools/2.2.3                 glimmer/3.0.2                      qiime/1.7.0
   bcftools/1.2                   glimmerhmm/3.0.2                   qiime/1.8.0
   beast/1.8.4                    gmake/3.82                         qiime/1.9.1          (D)
   bedtools/2.16.2                gmes/2.3e                          quast/2.3
   bioperl/00-2.1.8               grinder/0.5.4                      repseek/091209
   bioperl/1.6.901-p5162   (D)    gsnap/2013-11-27                   rocker/1.1.12
   biopython-py3/1.63             hdf5/1.8.13                        salmon/0.9.1
   biopython-py3/1.65             hisat2/2.0.4                       samtools/0.1.18
   biopython/1.60                 hisat2/2.1.0                (D)    samtools/1.2
   biopython/1.64                 hmmer2/2.3.2                       samtools/1.8         (D)
   biopython/1.66          (D)    hmmer3/3.0                         scipy-py3/0.13.1
   blasr/2014.07.09               htslib/1.8                         scipy/0.11.0rc2
   blast2go                       iprscan/4.8_db39                   seqtk/seqtk
   blat/35                        iqtree/1.5.5                       sga/0.10.1
   bowtie/0.12.9                  jre/1.6.0_39                       sina/1.2.11
   bowtie2/2.0.0-beta7            jre/1.7.0_11                       snap/2012-05-17
   bowtie2/2.0.2                  jre/1.7.0_51                       soapdenovo/1.05
   bowtie2/2.1.0                  jre/1.8.0_60                (D)    solexaqa/3.1.7
   bowtie2/2.2.3                  kallisto/0.45                      spades/3.6.0
   bowtie2/2.2.4                  legacy-blast/2.2.26                structure/2.3.4
   bowtie2/2.3.2           (D)    libfuse3/3.2.0                     structure/2.3.4.1    (D)
   bwa/0.5.10                     mafft/6.94                         tassel/5.0
   bwa/0.6.2                      matplotlib-py3/1.3.1               tophat/2.0.3.1
   bwa/0.7.4               (D)    matplotlib/1.2.0rc1         (D)    tophat/2.0.6
   bzip2c/1.0.6                   mavid/2.0.4                        tophat/2.0.9
   cafe/2.2                       mcl/12.068                         tophat/2.0.11
   cafe/3.1                (D)    meme/4.10.0                        tophat/2.0.13        (D)
   cdhit/4.6.1                    mercator/2013.01.11                trac/1.0.1
}}}