Applications
Applications installed on ALICE and SPECTRE. This list is not exhaustive and does not include common Linux utilities.
Application versions
Both ALICE and SPECTRE use Scientific Linux 5.4.
Generally there is a module available for each item in the list. Use the module command to see which versions of an application are available, for example for Fluent:
> module avail fluent --------------------- /cm/shared/modulefiles ------------------ fluent/13.0
Some applications have been built multiple times to suit the compilers available on the system. For example OpenMPI has been built for the GCC, Intel and Sun Studio compilers. A module exists for each one so you can choose the most appropriate.
Install an application
If you need to install an application on ALICE and SPECTRE, contact the IT Service Desk.
List of applications
You can find more information about the applications by following the links in the tables below. The links on the application names go to documentation at the University of Leicester. Links on the supplier names go to the supplier’s website.
A
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| ABINIT |
6.6.3 |
abinit/6.6.3 |
Free/OSS |
The ABINIT Group | Molecular dynamics simulation |
| Acrobat Reader |
9.4.1 |
Free |
Adobe |
PDF viewer |
|
| ActiveTcl |
8.5.8.2 |
activetcl/8.5.8.2 |
Free | ActiveState |
Tcl 8.5 distribution |
| Aladin |
7.5 |
Aladin/7.5 |
GPL v3 |
Aladin Sky Atlas |
Interactive software sky atlas |
| almost |
1.0.4 |
almost/1.0.4 |
Free/OSS |
Andrea Cavalli |
Molecular simulation toolkit |
| AMOS |
3.1.0 |
amos/3.1.0 |
Free/OSS |
AMOS Team |
Genetic assembly framework |
| Amber |
10 |
amber/10 |
Site licence |
Ambermd.org |
Amber molecular dynamics package |
| APT |
21.0.1 |
apt/21.0.1 apt/21.0 apt/21.1 |
Free/OS |
Space Telescope Science Institute |
Astronomer's proposal tool for HST and JWST |
| ARB |
5.1 (6213) |
arb/5.1-6213 |
Free/OSS |
Lehrstuhl für Mikrobiologie | Sequence visualisation |
| ATSAS |
2.5.0 |
ATSAS/2.5.0 |
Free |
EMBL Hamburg |
A program suite for small-angle scattering data analysis from biological macromolecules |
B
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| bcrypt |
1.1 |
bcrypt/1.1 |
Free/OSS |
Johnny Shelley |
Blowfish encryption/decryption |
| BEAM |
4.9.0.1 |
beam/4.9.0.1 |
Free/OSS |
Team BEAM |
Satellite raster data analysis |
| BEAT |
6.7.0 6.5.0 6.2.0 |
beat/6.7.0 beat/6.5.0 beat/6.2.0 |
Free/OSS |
S & T |
Basic Envisat Atmospheric Toolbox |
| bedtools |
2.15.0 |
bedtools/2.15.0 |
Fress/OSS |
Aaron Quinlan | Flexible suite of utilities for comparing genomic features |
| BioPerl |
1.6.1 |
bioperl/1.6.1 |
Free/OSS |
Open Bioinformatics Foundation |
Perl packages for bioinformatics |
| blas | March 2007 |
blas/gcc/64/1 blas/intel/64/1 |
Free/OSS | Netlib |
Basic Linear Algebra Sub-programs |
| BLAST |
2.2.23 |
blast/2.2.23 |
Free |
NCBI |
Basic Local Alignment Search Tool |
| BLAST+ |
2.2.25 |
blast+/2.2.25 |
Free | NCBI | C++ Implementation of BLAST |
| Boost |
1.53.0 |
boost/1.53.0 |
Free/OSS |
Boost Community |
C++ libraries |
| Bowtie |
2.0.0-beta7 2.0.0 0.12.7 |
bowtie/2.0.0-beta7 bowtie/2.0.0 bowtie/0.12.7 |
Free/OSS |
Johns Hopkins Bloomberg School of Public Health | Short DNA sequence aligner |
| BWA |
0.6.2 0.5.9 |
bwa/0.6.2 bwa/0.5.9 |
Free/OSS |
BWA Team |
Burrows-Wheeler Aligner |
C
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| Cadaver |
0.22.3 |
Free/OSS |
Cadaver team |
WebDAV client |
|
| cairo graphics |
1.10.2 |
cairo/1.10.2 |
Free/OSS |
CairoGraphics |
Graphics Libraries |
| CAStep |
6.1 |
CASTEP/6.1 |
Restricted |
RAL |
Material Property Calculation |
| CASUTools |
1.0.24 |
casutools/1.0.24 |
Free/OSS |
CASUTools team |
CASU pipeline processing tools |
| CDO |
1.5.3 |
cdo/1.5.3 |
Free/OSS |
CDO |
Climate Data Operators |
| cgns | 2.5.4 | cgns/2.5.4 |
Free/OSS | CGNS Steering Committee |
CFD General Notation System |
| CIAO |
4.5 |
ciao/ciao-4.5 |
Free/OSS |
Chandra team |
Chandra X-ray Data Analysis Software (includes CALDB) |
| CleaveLand |
3.0.1 |
cleaveland/3.0.1 |
Free/OSS |
Penn State University |
RNA analysis |
| CNS |
1.3 |
cns/1.3 |
Free/OSS |
CNS team |
Crystallography and NMR system |
| CODA | 2.2 | coda/2.2 |
Free/OSS | ESA |
Python EOS Toolbox |
| CPL (Common Pipeline Library) | 6.2 | Free/OSS | ESO | Astronomical data-reduction task ISO-C libraries | |
| CPMD |
3.15.3 |
CPMP/3.15.3 |
Restricted | CPMD Consortium |
Density Functional Theory |
| CS_ROSETTA |
1.01 |
cs-rosetta/1.01 |
Free/OSS |
CS_ROSETTA team |
Chemical shifts based protein structure prediction using ROSETTA |
| Cyana |
2.1 |
cyana/2.1 |
Restricted |
LA Systems, Inc. |
Automated structure calculation of biological macromolecules |
| Cytoscape |
2.8.1 |
cytoscape/2.8.1 |
Free/OSS |
NRNB |
Network visualisation |
D
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| DIRAC |
10 |
dirac/10 |
See terms |
DIRAC team |
Molecular modelling |
| Dialign-tx |
1.0.2 |
dialign-tx |
LGPL |
Uni. of Gottingen |
|
| doxygen1 |
1.4.7 |
Free/OSS | Dimitri van Heesch | Source code documentation system |
|
| Doxygen |
1.8.3.1 | doxygen/1.8.3.1 |
Free / OSS |
Dimitri van Heesch |
Recent version of documentation generator |
| DS9 | 6.2 7.2 |
ds9/6.2 ds9/7.2 |
Free/OSS | Smithsonian Astrophysical Observatory | Astronomical imaging and data visualization |
E
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| Eclipse |
3.6.2 |
eclipse/3.6.2 |
Free/OSS |
The Eclipse Foundation |
SDE |
| EMBOSS |
6.4.0 6.3.1 |
emboss/6.4.0 emboss/6.3.1 |
Free/OSS |
EMBOSS |
Molecular Biology software suite. Includes Jemboss 1.5 |
| ENVI |
4.7 |
envi/4.7 |
200 licences |
ITT |
Geospatial imagery analysis |
| ESO-MIDAS | 1.3 | esomidas/1.3 | Free/OSS | ESO | Astronomy image processing / data reduction |
| EsoRex | 3.9.6 | esorex/3.9.6 | Free/OSS | ESO |
CPL (Common Pipeline Library) Recipe Execution Tool |
| exonerate |
2.2.0 |
exonerate/2.2.0 |
Free/OSS |
Guy Slater |
Pairwise sequence comparison / alignment tool |
F
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| FASTA |
3.6 |
fasta/3.6 |
Free/OSS |
University of Virginia |
Protein / DNA search tool |
| FASTX-Toolkit |
0.0.13.2 |
fastx_toolkit/0.0.13.2 |
Free/OSS | Assaf Gordon + contributors |
Short-Reads FASTA/FASTQ preprocessing |
| fastsimcoal | 1.1.2 | fastsimcoal/1.1.2 | Free | University of Berne | Genomic diversity simulator |
| Ferret |
6.6.4 |
ferret/6.6.4 |
Free/OSS |
NOAA/OAR/PMEL | Data visualisation |
| FinchTV |
1.3.1 |
finchtv/1.3.1 |
Free |
Geospiza, Inc. |
DNA sequence trace viewer |
| Firefox |
3.6.13 |
Free/OSS |
Mozilla Foundation |
Web browser |
|
| FL (Fawlty Language) |
0.79a |
fl/0.79a |
Free/OSS |
Lajos Földy | IDL clone |
| Fluent |
13.0 |
fluent/13.0 |
25 users |
ANSYS |
CFD |
| fftw2 |
2.1.5 |
fftw/gcc/2.1.5 fftw/intel/2.1.5 |
Free/OSS | FFTW |
Discrete fourier/cosine/sine transform library |
| fftw3 |
3.2.2 |
fftw/gcc/3.2.2 fftw/intel/3.2.2 |
Free/OSS |
FFTW |
Discrete fourier/cosine/sine transform library |
| FSL |
5.0.22 |
fsl/5.0.22 |
Free/OSS |
University of Oxford | FMRIB brain imaging tools |
G
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| G95 |
0.93 |
g95/0.93 |
Free/OSS |
The G95 Project |
Fortran 95 compiler |
| GAMESS (US) |
2011-08-11 |
gamess-us/2011-08-11 |
Free |
GAMESS (US) Project |
A general ab initio quantum chemistry package |
| GASGANO | 2.4.3 | gasgano/2.4.3 | Free/OSS | ESO | VLT compliant telescope data file organiser |
| GATK | 2.3-9 |
gatk/2.3-9 | Free - restricted |
Broad Institute |
Genome Analysis Toolkit |
| Gaussian |
g03e01 |
gaussian/g03e01 |
Restricted |
Gaussian, Inc. |
Electronic structure modelling |
| Gauss |
12.1 12 11 |
gauss/gauss12.1 gauss/gauss12 gauss/gauss11 |
6 Users |
Aptech |
Mathematical and statistical data analysis environment |
| Gauss Runtime |
12.1 12 11 |
gauss/gaussruntime12.1 gauss/gaussruntime12 gauss/gaussruntime11 |
Free | Aptech |
Gauss Runtime for compiled Gauss Code |
| GCC (GNU Compiler Collection) |
4.1.1 4.3.4 4.6.2 4.7.0 4.8.0 |
gcc/4.1.1 gcc/4.3.4 gcc/4.6.2 gcc/4.7.0 gcc/4.8.0 |
Free/OSS |
GNU |
C/C++/Fortran compilers |
| GDAL |
1.9.2 (with Python2.6.5 bindings) 1.9.0 |
gdal/1.9.2 gdal/1.9.0 |
Free/OSS |
Frank Warmerdam / GDAL developers |
Translator library for raster geospatial data formats |
| GDB (Gnu Debugger) |
7.0.1 |
Free/OSS |
GNU |
Program debugger |
|
| GDL (GNU Data Language) |
0.9.3 0.9.2 0.9 0.9rc4 |
gdl/0.9.3 gdl/0.9.2 gdl/0.9 gdl/0.9rc4 |
Free/OSS |
GNU |
IDL clone |
| GHC |
6.12.3 |
ghc/6.12.3 |
Free/OSS |
Glasgow University |
The Glasgow Haskell Compiler |
| GHMM |
2011-03-02 |
ghmm/2011-03-02 |
Free/OSS |
Rutgers University |
General hidden Markov model library |
| Ghostview |
3.6.2 |
Free/OSS |
Ghostscript team |
PostScript viewer |
|
| Ghostscript |
9.04 |
ghostscript/9.04 |
Free/OSS |
Ghostscript Team |
PostScript interpreter |
| gifsicle |
1.60 |
gifsicle/1.60 |
Free/OSS |
Eddie Kohler |
Animated GIF creator |
| git |
1.7.2 |
git/1.7.2 |
Free/OSS |
Git |
Version control software |
| Glimmer |
3.02 |
glimmer/3.02 |
Free/OSS | University of Maryland |
Genetics |
| GMT |
4.5.7 |
gmt/4.5.7 |
Free/OSS |
GMT Team |
Generic Mapping Tools |
| gnuplot |
4.4.2 4.0 |
gnuplot/4.4.2 |
Free/OSS |
Gnuplot team |
Data visualisation |
| Grace |
5.1.22 |
grace/5.1.22 |
Free/OSS |
Grace team |
Data visualisation |
| GROMACS |
4.5.1 |
gromacs/4.5.1 |
Free/OSS |
Molecular dynamics |
|
| GotoBLAS2 |
1.13 |
gotoblas/gcc/1.13 gotoblas/gcc41/1.13 gotoblas/intel/1.13 |
Free/OSS |
TACC |
Optimised basic linear algebra sub-programs |
| GSL (GNU Scientific Library) |
1.14 |
gsl/gcc/1.14 gsl/intel/1.14 |
Free/OSS |
GNU |
Scientific library for C/C++. |
| GTOOL |
0.7.5 0.7.0 |
gtool/0.7.5 gtool/0.7.0 |
Free |
University of Oxford |
Genotype transform tool |
H
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| HADDOCK |
2.1 |
haddock/2.1 |
Free/OSS |
Bijvoet Center for Biomolecular Research | High ambiguity driven biomolecular docking |
| HDF5 |
1.8.5 1.8.7 |
hdf5/intel/1.8.5 hdf5/gcc/1.8.7 hdf5/intel/1.8.7 hdf5-par/gcc/1.8.7 hdf5-par/intel/1.8.7 |
Free/OSS |
HDF Group |
Data model library |
| HDF4 |
4.2.6 |
hdf4/intel/4.2.6 hdf4/gcc/4.2.6 |
Free/OSS | HDF Group | |
| HEASoft |
6.12 6.11 6.10 |
heasoft/6.12 heasoft/6.11 heasoft/6.10 |
Free/OSS |
NASA / HEASARC |
X-Ray Astronomy / FITS file tools |
I
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| IDL |
8.2 8.1 8.0 7.0 |
idl/idl82 idl/idl81 idl/idl80 idl/idl70 |
Restricted |
ITT VIS |
Data analysis programming language |
| IDL Astronomy User's Library |
11 Feb 2013 |
idlastro/20130211 |
Free / BSD 2 |
NASA Goddard Space Flight Center |
Low-level IDL astronomy software |
| iHS |
2009 |
ihs/2009 |
Free/OSS |
Pritchard Lab |
Genome analysis of signals of selection |
| ImageMagick1 |
6.7.4-0 6.2.8 |
ImageMagick/6.7.4-0 | Free/OSS |
ImageMagick team |
Bitmap image tools |
| Impute2 |
2.3.0 2.1.2 2.2.2 |
impute2/2.3.0 impute2/2.1.2 impute2/2.2.2 |
Free |
University of Oxford |
Genotype imputation and phasing |
| Info-ZIP |
zip 3.0, unzip 6.00 |
zip64/1.00 |
Free/OSS |
Info-ZIP team |
File compression and decompression |
| Intel Compilers |
11.1 12.0.0 12.0.2 12.1.0 12.1.3 |
intel/64/compiler/11.1.072 intel/64/compiler/12.0.0 intel/64/compiler/12.0.2 intel/64/compiler/12.1.0 intel/64/compiler/12.1.3 |
5 users |
Intel |
Intel C/C++/Fortran compilers |
| Intel ITAC |
8.0.1 |
intel/64/itac/8.0.1 |
ALICE |
Intel |
Intel trace analyser and collector |
| Intel MPI |
3.2.2 4.0.0 4.0.1 |
intel/64/impi/3.2.2 intel/64/impi/4.0.0 intel/64/impi/4.0.1 intel/64/impi/4.0.3 |
ALICE |
Intel |
Intel MPI parallel programming libraries |
| Intel MKL |
10.2.5 10.3.0 10.3.7 10.3.9 |
intel/64/mkl/10.2.5 intel/64/mkl/10.3.0 intel/64/mkl/10.3.7 intel/64/mkl/10.3.9 intel/64/mkl/10.3.10 |
ALICE |
Intel |
Intel math kernel libraries |
| iPython |
0.12 | 0.12 | ALICE |
iPython |
Python Shell |
| ISIS | 1.6.2-18 | isis/1.6.2-18 | Free/OSS | MIT | Interpretation and analysis of high resolution X-ray spectra |
J
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| Java JDK |
1.7 1.60u29 |
java/1.7.0 |
Free |
Oracle |
Programming language |
| Jemboss |
1.5 |
emboss/6.4.0 |
See EMBOSS |
||
| joe |
3.4 |
Free/OSS |
Joseph Allen |
Text editor |
K
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| KiCAD |
2011-11-30 |
kicad/2011-11-30 |
Free/OSS |
KiCad Developers Team | EDA (Electronic Design Automation) Suite |
L
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| LAGAN Toolkit |
2.0 |
lagan/2.0 |
Free/OSS |
LAGAN team |
Sequence alignment toolkit |
| LAPACK |
3.2.1 |
lapack/gcc/64/3.2.1 lapack/intel/64/3.2.1 |
Free/OSS |
Netlib |
Linear algebra routines for F90 |
| LASTZ |
1.02.00 |
lastz/1.02.00 |
Free/OSS |
Miller Lab, Penn State University |
Sequence alignment tool |
| LocusZoom |
1.1 |
locuszoom/latest |
Free/OSS |
LocusZoom |
Genome Results Plotting Tool |
| LyX |
2.0.0 |
lyx/2.0.0 |
Free/OSS |
LyX contributors |
Tex / LaTeX document processor |
M
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| MaM |
1.4.2 |
MaM/0.7.1 |
Free/OSS |
Can Alkan |
Multiple alignment Manipulator |
| Maq |
0.7.1 |
maq/0.7.1 |
Free/OSS |
Heng Li |
Sequence mapping assembler |
| MATLAB |
2013a (8.1.0.604) 2011b (7.13.0.564) |
matlab/2013a matlab/2011b |
200 users |
MathWorks |
High level programming language |
| Matplotlib |
1.1.0 |
matplotlib/1.1.0 |
Free/OSS |
Sourceforge |
python plotting tool |
| Mencoder |
2010-10-20 |
mencoder/2010-10-20 |
Free/OSS |
Mplayer team |
Audio/video encoder |
| Mercurial |
1.7.3 |
mercurial/1.7.3 |
Free/OSS |
Mercurial team |
Source control management |
| Metaxa |
1.0.2 |
metaxa/1.0.2 |
Free/OSS |
University of Gothenburg |
|
| MOPEX |
18.5 |
mopex/18.5 |
Free |
Spitzer Science Center |
Image and MIPS SED reduction/analysis |
| Mothur |
1.21.0 |
mothur/1.21.0 |
Free/OSS |
Patrick Schloss |
Microbial ecology bioinformatics tool |
| mrCaNaVaR |
0.34 |
mrcanavar/0.34 |
Free/OSS |
mrCaNaVaR team |
micro-read Copy Number Variant Regions |
| mrFAST |
2.1.0.3 |
mrfast/2.1.0.3 |
Free/OSS |
mrFAST team |
Micro Read Fast Alignment Search Tool |
| MUMPS |
4.10.0 |
Free |
Ens de Lyon |
A parallel sparse solver library |
|
| muscle |
3.8.31 |
muscle/3.8.31 |
Free/OSS |
Robert C. Edgar |
Multiple sequence alignment |
N
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| NAG |
Various |
nag/product |
Commercial |
NAG |
Numerical libraries for C, Fortran |
| NASA Baselibs |
2.2.0 |
nasa-baselibs/2.2.0 |
Free/OSS |
NASA |
A collection of libraries used by the GEOS5 software |
| NetCDF |
4.1.2 |
netcdf/gcc/4.1.2 netcdf/intel/4.1.2 netcdf-par/gcc/4.1.2 netcdf-par/intel/4.1.2 |
Free/OSS |
Unidata |
Data model library |
| Netpbm1 |
10.35.58 |
Free/OSS |
Netpbm team |
Bitmap image tools |
|
| NJplot |
2.3 |
njplot/2.3 |
Free, cite if work published |
Pôle Bioinformatique Lyonnais |
Phylogenetic tree drawing |
| NMRPipe | 1.01 |
nmrpipe/1.01 |
Free |
Frank Delaglio |
NMR spectroscopic data analysis |
O
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| OpenBUGS |
3.1.2 |
openbugs/3.1.2 |
Free/OSS |
OpenBUGS team |
Bayesian statistics using Markov chain Monte Carlo simulation |
| OpenMPI |
1.4.2 |
openmpi/gcc/1.4.2 openmpi/intel/1.4.2 openmpi/sun/1.4.2 |
Free/OSS |
OpenMPI team |
MPI parallel programming interface |
| Orbit Visualization Tool (OVT) |
2.3_4 |
ovt/2.3_4 |
Free, must be cited in publication | OVT Team |
Visualization of satellite orbits in the Earth's magnetic field |
P
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| ParaView* |
3.8.0 |
paraview/3.8.0 |
Free/OSS |
ParaView team |
Visualisation |
| PDL |
2.4.9 |
Free/OSS |
PDL community |
Perl data language |
|
| Perl |
5.14.1 5.8.8 |
perl/5.14.1 |
Free/OSS |
Perl community |
Perl programming language interpreter |
| PGPlot** |
5.2 |
pgplot/5.2 |
Free/OSS |
CalTech |
Data visualisation |
| PHASE | 2.1.1 | phase/2.1.1 | See terms |
University of Washington |
Reconstruction of haplotypes from population data. |
| PHENIX |
1.7.2-869 |
phenix/1.7.2-869 |
Free, must be cited in publications |
PHENIX community |
Python-based Hierarchical ENvironment for Integrated Xtallography |
| PHENIX |
1.7.3-928 |
phenix/1.7.3-928 |
Free, must be cited in publications |
PHENIX community |
Python-based Hierarchical ENvironment for Integrated Xtallography |
| Phrap |
1.090518 |
phrap/1.090518 |
Academic User Agreement |
Phil Green |
DNA sequencing |
| Phred |
020425 |
phred/020425 |
Academic User Agreement | Phil Green / Brent Ewing | DNA sequencing |
| picard |
1.86 | picard/1.86 | Free/OSS |
Java tools for next generation sequencing data |
|
| PLATO |
1.2.0 |
plato/1.2.0 |
Free/OSS |
Center for System Genomics, Penn State University |
PLatform for the Analysis, Translation and Organisation of large scale genome data |
| plink |
1.0.7 |
plink/1.0.7 |
Free/OSS |
Shaun Purcell |
Whole genome association analysis tool |
| PLplot |
5.9.6 |
plplot/5.9.6 |
Free/OSS |
PLplot team |
Data visualisation |
| PolSARpro |
4.1.5 |
plosarpro/4.1.5 |
Free |
ESA |
Polarimetric SAR Data Processing and Educational Tool |
| Python |
3.1.2 2.7.3 2.6.5 2.4.3 |
python/3.1.2 python/2.7.3 python/2.6.5 python/2.4.3 |
Free/OSS |
Python Software Foundation | Programming language |
**Please only use PGPLOT if there's absolutely no alternative. It's no longer maintained and becomes increasingly harder to support as operating systems develop.
Q
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| QCTOOL |
1.1 |
qctool/1.1 |
Free |
QCTOOL Team |
Control of GWAS data sets |
| QDOAS |
1.162 1.165 1.168 2.0 |
QDOAS/1.162 QDOAS/1.165 QDOAS/1.168 QDOAS/2.0 |
Free/OSS |
BIRA-IASB and S[&]T | atmospheric chemistry, differential optical absorption spectroscopy |
| qiime |
1.6.0 1.3.0 1.2.1 |
qiime/1.6.0 qiime/1.3.0 qiime/1.2.1 |
Free/OSS |
qiime |
pipeline for performing microbial community analysis |
R
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| R |
2.15.2 2.15.1 2.14.2 2.14.0 2.13.0 |
R/2.15.2 R/2.15.1 R/2.14.2 R/2.14.0 R/2.13.0 |
Free/OSS |
R team |
Statistical computing |
| RCS1 |
5.7 |
Free/OSS |
GNU |
Revision control system |
|
| RepeatMasker |
3.2.8 |
repeatmasker/3.2.8 |
Various |
Institute for Systems Biology |
Sequence screening tool |
| RepeatScout |
1.0.5 |
repeatscout/1.0.5 |
Free/OSS |
RepeatScout team |
DNA repetitive sequence search |
| ROOT |
5.30.01 5.26.00 |
root/5.30.01 root/5.26.00 |
Free/OSS |
CERN |
Object oriented programming environment |
| Rosetta |
3.3 |
rosetta/3.3 |
Academic License |
RosettaCommons Members |
Protein library suite |
| Ruby |
1.8.5 |
Free/OSS |
Ruby community |
Programming language |
S
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| SAMtools |
0.1.17 |
samtools/0.1.17 |
Free/OSS |
SAMtools team |
SAM-format sequence alignment tools |
| SHAPEIT |
1.416 |
shapeit/1.416 |
Free |
Olivier Delanneau | Haplotype inference tool |
| SNPtest |
2.4.1 2.2.0 |
snptest/2.4.1 snptest/2.2.0 |
Free |
University of Oxford |
SNP analysis |
| SOLAR |
4.3.1 |
solar/4.3.1 |
Some features require free registration |
SOLAR |
Genetic variance components analysis |
| Spitzer "Pride" (Spot/Leopard) |
19.7.2 |
spitzer/19.7.2 |
Free |
Spitzer Science Center |
Observation planning/querying |
| SQLite |
3.4.17.1 |
sqlite/3.4.17.1 |
Free/OSS |
SQLite team |
SQL database engine |
| Stacks | 0.99991 | stacks/0.99991 | Free/OSS |
University of Oregan |
Building loci from short-read genome sequences |
| Staden |
2.0.0b8 |
staden/2.0.0b8 |
Free/OSS |
Sourceforge |
DNA sequence assembly (Gap4 and Gap5), editing and analysis tools |
| Starlink |
Kapuahi 2012-09-17 Namaka 2011-02-07 |
starlink/2012-09-17 starlink/2011-02-07 |
Free/OSS |
Starlink team |
Astronomical data processing |
| SExtractor |
2.8.6 |
sextractor/2.8.6 |
Free/OSS |
Emmanuel Bertin |
Builds a catalogue of objects from an astronomical image |
| STATA MP8 |
12 11 |
stata/12/mp8 stata/11/mp8 |
Restricted |
STATA |
Statistics, graphs and data management |
| Subversion1 |
1.6.12 |
Free/OSS |
Apache Software Foundation |
Version control client |
|
| Sun Studio |
12.1 |
sunstudio/12.1 |
Free |
Oracle |
C/C++/Fortran compilers and IDE |
| SuperMongo |
2.4.36 |
supermongo/2.4.36 |
Restricted |
Robert Lupton and Patricia Monger |
Data visualisation |
| SWIG |
2.0.0 1.3.40 |
swig/2.0.0 swig/1.3.40 |
Free/OSS |
SWIG team |
Simplified Wrapper and Interface Generator |
T
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| Tabix |
0.25 |
tabix/0.2.5 |
Free/OSS |
SAM tools team |
Generic indexer for TAB-delimited genome position files |
| Target Finder |
1.6 |
targetfinder/1.6 |
Free |
Carrington Lab |
RNA analysis |
U
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| UDUNITS |
2.1.17 |
udunits/2.1.17 |
Free/OSS |
Unidata |
Unit definition and value conversion utility and library. |
V
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| Valgrind |
3.5.0 |
Free/OSS |
Valgrind team |
Software analysis tool |
|
| Velvet |
1.2.07 |
velvet/1.2.07 |
Free/OSS |
Daniel Zerbino / Ewan Birney |
Sequence assembler for very short reads |
| VTK |
5.6.1 |
vtk/5.6.1 |
Free/OSS |
Kitware, Inc. |
Visualisation |
W
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| WCSTools | 3.8.7 |
wcstools/3.8.7 |
Free/OSS |
SAO |
World Coordinate Systems tools |
| wxWidgets |
2.8.12 |
wxwidgets/2.8.12 |
Free/OSS |
wxWidgets team |
C++ application library |
X
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| Xfig |
3.2.5b |
Xfig/3.2.5b |
Free/OSS |
Xfig team |
Illustration tool |
| XMM SAS |
12.0.1 |
xmmsas/12.0.1 |
Free |
ESA |
XMM-Newton Science Analysis System |
0-9
| Software | Version | Module | Licence | Supplier | Description |
|---|---|---|---|---|---|
| 3D Dock Suite (FTDock) |
2.0 |
3d_dock/2.0 |
FTDock (Free/OSS) |
ICRT |
Protein docking |
| 454 Sequencing |
2.6.0 2.5.3 |
gs454/2.6.0 gs454/2.5.3 |
Commercial |
Roche |
454 Gene sequencer, post-processing and analysis |
Notes
1. Login nodes only.
