| Application Name | Versions | Module Names |
| AFNI / SUMA | 7 | AFNI/7 |
| ANNOVAR | 20130509 | annovar/20130509 |
| ANTS (Advanced Normalization ToolS) | 1.9.x (SVN) | ANTS/1.9.x |
| APT (Affymetrix Power Tools) | 1.15.1 | APT/1.15.1 |
| AutoDock | 4.2.5-1 | autodock/4.2.5-1 |
| AutoDock Tools (MGL Tools) | 1.5.6 | mgltools/1.5.6 |
| AutoDock Vina | 1.1.2 | vina/1.1.2 |
| BEAGLE | 3.3.2 | beagle/3.3.2 |
| BLAT | 0.34 | blat/0.34 |
| boost | 1.53.0 | boost/1.53.0 |
| Bowtie | 1.0.0, 2.1.0 | bowtie/1.0.0, bowtie2/2.1.0 |
| BRugs | 0.8-1 | Part of R |
| bwa (Burrows-Wheeler Aligner) | 0.5.9, 0.7.4 | bwa/0.5.9, bwa/0.7.4 |
| CellProfiler | 2.0 | CellProfiler |
| chiamo | 0.2.1 | chiamo/0.2.1 |
| cufflinks | 2.1.1 | cufflinks/2.1.1 |
| DTIPrep | 1.2 | DTIPrep/1.2 |
| eigensoft | 4.2 | eigensoft/4.2 |
| Farsight ToolKit | 0.4.4 | farsight/0.4.4 |
| ffmpeg | GIT | ffmpeg/52570-g6b222ea |
| FFTW2 | 2.1.5 | fftw2/{gcc,open64}/64/{double,single}/2.1.5 |
| FFTW3 | 3.3.1 | fftw3/{gcc,open64}/64/{double,single}/3.3.1 |
| FSL (FMRIB Software Library) | 5.0.2.2 | fsl/5.0.2.2 |
| GATK (Genome Analysis ToolKit) | 2.5-2 | gatk/2.5-2 |
| gtool | 0.7.5 | gtool/0.7.5 |
| hapgen | 2.2.0 | hapgen/2.2.0 |
| Haploview | 4.2 | haploview/4.2 |
| HLA-IMP | 1.3.3 | HLA-IMP/1.3.3 |
| homer | 4.2 | homer/4.2 |
| impute | 2.3.0 | impute/2.3.0 |
| Intel (compilers, etc.) | 2013.3.163 | intel/2013.3.163 |
| ITK (Insight ToolKit) | 4.4.0 (GIT) | itk/4.4.0 |
| JAGS (Just Another Gibbs Sampler | 3.3.0 | jags/3.3.0 |
| KING (Kinship-based INference for Gwas) | 1.4 | king/1.4 |
| LAMP-LD (Local Ancestry in adMixed Populations) | 1.0 | LAMP-LD/1.0 |
| libsvm | 3.17 | libsvm/3.17 |
| Matlab | 2013a | matlab/2013a |
| MayaChemTools | 20130418 | mayachemtools/20130418 |
| Maya / MentalRay | 2011 | maya/2011, maya/2012 |
| miRDeep2 | miRDeep2 | |
| miRExpress | 2.1.4 | miRExpress/2.1.4 |
| mricron | 12/2012 | mricron/2012_12 |
| Mx | 1.54a | mx/1.54a |
| NetCDF | 4.2 | netcdf/{gcc,open64}/64/4.2 |
| NONMEM | 7.2.0 | |
| Open Babel | 2.3.2 | openbabel/2.3.2 |
| OpenBUGS | 3.2.2 | openbugs/3.2.2 |
| PeakSplitter | 0.1 | PeakSplitter/0.1 |
| pedsys | 2.0 | pedsys/2.0 |
| Perl & Padre (Perl IDE) | 5.16.3 | perl/5.16.3 |
| picard | 1.89 | picard/1.89 |
| PLINK/gPLINK | 1.07 | plink/1.07 |
| protobuf - Protocol Buffers | 2.4.1 | protobuf/2.4.1 |
| Qt | 4.8.4 | qt/4.8.4 |
| R | 2.15.3, 3.0.0 | R/2.15.3, R/3.0.0 |
| R2WinBUGS | 2.1-19 | Part of R |
| randfold | 2.0 | randfold/2.0 |
| samtools | 0.1.19 | samtools/0.1.19 |
| slicer | 4.2.0 | slicer/4.2.0 |
| SHAPEIT (Segmented HAPlotype Estimation and Imputation Tool) | 2.644 | shapeit/2.644 |
| snptest | 2.4.1 | snptest/2.4.1 |
| SOLAR (Sequential Oligogenic Linkage Analysis Routines) | 6.6.2 | solar/6.6.2 |
| Subversion | 1.7.10,1.8.0 | subversion/1.7.10,subversion/1.8.0 |
| SQUID | 1.9g | squid/1.9g |
| tabix | 0.2.6 | tabix/0.2.6 |
| Tophat | 2.0.8b | tophat/2.0.8b |
| Trinity (RNA-Seq De novo Assembly) | 2013-02-25 | trinityrnaseq/20130225 |
| VAAST (Variant Annotation, Analysis & Search Tool) | 1.0.3 | VAAST/1.0.3 |
| vcftools | svn, 0.1.10 | vcftools/svn, vcftools/0.1.10 |
| ViennaRNA | 2.1.2 | ViennaRNA/2.1.2 |
| VTK (Visualization ToolKit) | 5.10.1 (GIT) | vtk/5.10.1 |
| WebLogo | 2.8.2 | WebLogo/2.8.2 |
| WinBUGS | 1.4.3 |