Personal tools

Applications

A list of the applications installed on ALICE and SPECTRE

This list is not exhaustive, common Linux utilities are not listed for example. Both ALICE and SPECTRE use Scientific Linux 5.4.

Generally there is a module available for each item in the list, and all module names are in lower case. For example, to see which version(s) of Fluent are available:

> module avail fluent
--------------------- /cm/shared/modulefiles ------------------
fluent/13.0

Some applications have been built multiple times with different compilers to suit the various compilers available on the system. OpenMPI for example has been built for each of GCC, Intel and Sun Studio compilers, and a module exists for each one so that the most appropriate can be chosen.

Within each application's record in the tables below, a link on the application name itself will be to our own application-specific documentation. A link on the supplier name will be to the application's website on the internet.

Requests for applications to be installed on the HPC systems should be sent to the Service Desk.

Jump to: A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | 0-9

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
almost
1.0.4
almost/1.0.4
Free/OSS
Andrea Cavalli
Molecular simulation toolkit
Amber
10
amber/10
Site licence
Ambermd.org
Amber molecular dynamics package
ARB
5.1 (6213)
arb/5.1-6213
Free/OSS
Lehrstuhl für Mikrobiologie Sequence visualisation

B

Software
Version
Module
Licence
Supplier
Description
BEAM
4.9.0.1
beam/4.9.0.1
Free/OSS
Team BEAM
Satellite raster data analysis
BEAT
6.5.0
6.2.0
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
Bowtie
0.12.7
bowtie/0.12.7
Free/OSS
Johns Hopkins Bloomberg School of Public Health Short DNA sequence 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.
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
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
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

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
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
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

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
Gaussian
g03e01
gaussian/g03e01
Restricted
Gaussian, Inc.
Electronic structure modelling
Gauss
12
11
gauss/gauss12
gauss/gauss11
2 Users
Aptech
Mathematical and statistical data analysis environment
Gauss Runtime
12
11
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
gcc/4.1.1
gcc/4.3.4
gcc/4.6.2
Free/OSS
GNU
C/C++/Fortran compilers
GDAL
1.9.0
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)
0.9.2
0.9
0.9rc4

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
8.1
8.0
7.0
idl/idl81
idl/idl80
idl/idl70
Restricted
ITT VIS
Data analysis programming language
ImageMagick1
6.7.4-0
6.2.8

ImageMagick/6.7.4-0 Free/OSS
ImageMagick team
Bitmap image tools
Impute2
2.1.2
2.2.2
impute2/2.1.2
impute2/2.1.2
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
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
ALICE
Intel
Intel math kernel libraries
iPython
0.12 0.12 ALICE
iPython
Python Shell

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
Maq
0.7.1
maq/0.7.1
Free/OSS
Heng Li
Sequence mapping assembler
MATLAB
2011b (7.13.0.564)
2010a (7.10.0.499)
2007b (7.5.0.338)
matlab/2011b
matlab/2010a
matlab/2007b
150 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

Mothur
1.21.0
1.19.0
1.17.3
1.12.3
mothur/1.21.0
mothur/1.19.0
mothur/1.17.3
mothur/1.12.3
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

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
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
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
2.4.3

Free/OSS
Python Software Foundation
Programming language
Python
3.1.2
2.6.5
python/3.1.2
python/2.6.5
Free/OSS
Python Software Foundation Programming language

*Currently not parallelised.

**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
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
1.3.0
1.2.1
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
2.14.2
2.13.0
R/2.14.2
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
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
2.2.0
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
Staden
2.0.0b8
staden/2.0.0b8
Free/OSS
Sourceforge
DNA sequence assembly (Gap4 and Gap5), editing and analysis tools
Starlink
Namaka 2011-02-07
starlink/2011-02-07
Free/OSS
Starlink team
Astronomical data processing
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
VTK
5.6.1
vtk/5.6.1
Free/OSS
Kitware, Inc.
Visualisation

W

Software
Version
Module
Licence
Supplier
Description
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

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.