Software

Software

The table below shows an overview of the application software that is available on each of the Notur systems. Select a discipline from the menu to restrict the list of software to relevant entries.

The presence of application software for a specific system as shown in the table usually means that the software is centrally installed and available for all users of the system. However, certain restrictions may apply for software that has specific conditions for usage in the license agreement. The software can typically be used for academic non-commercial purposes. For other usage, in particular commercial usage, make sure that you are informed about the details of the software license.

The table below is automatically generated from the software modules that are available on the systems. Some of the names have architecture-specific names, while others have not. If a particular software package does not have an entry for a system, it could be that a) the software is not (centrally) installed on that system, or b) running the software on that system is discouraged, or c) it is not allowed to execute the software on that system.

The table represents the current situation fairly accurately, but may contain incomplete or out-of-date entries. Application software installed by users is not included.

Please do not install your own copies of software that is already (centrally) installed. In case you need access to a different version of the software, please contact the support staff for the system in question.

User-installed software. In case you have application sotware that you wish to install and execute on the Notur systems, but you are unsure which system is most suitable, we strongly advise you to contact the support staff.

Selecting a package name in the left column of the table expands the entry with a short description. A green icon links to the home page of the software. Any pages describing a given installation are linked from the corresponding available version.

  • Version number: The software is installed on the machine with the version(s) listed available.
  • x: The software is installed on the machine, but version information is not available.

Please contact the support staff for the system in question for information about the availability of application software that is not listed here, especially if you consider to apply for access to this system.

All software

  

Abel

Gardar

Hexagon

Stallo

Vilje

454apps   2.9
2.8
2.7
2.6
2.3
2.5.3
2.0.01.02
1.1.03.24
    
abaqus      6.11-2
A suite of software applications for finite element analysis.
AbInit    7.6.1
 
abyss  1.3.4
  1.2.3
1.2.1
  
ACML    4.4.0
4.3.0
4.2.0
  
AMD Core Math Library
ADF  2010.02b
2012.01b
2013.01
2013.01b
   2013.01d
2013.01a
ADF is the Amsterdam Density Functional program system for electronic structure calculations.
ADF/BAND    2012.01c
 
alglib    3.0
 
ALGLIB is a cross-platform numerical analysis and data processing library.
ALLPATH-LS    48686
 
allpathslg   48777
    
AMBER  12
  12
12
A package of molecular simulation programs.
amos   3.1.0
    
AmpliconNoise  1.29
1.25
    
AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons.
ANSYS    13.0
 
ANTLR    2.7.7
2.7.7
2.7.7
ANTLR, ANother Tool for Language Recognition, is a language tool that provides a framework for constructing recognizers, interpreters, compilers, and translators from grammatical descriptions containing actions in a variety of target languages.
ANTS    1.9.1
 
apprentice2    5.1.3
5.1.2
5.0.1
  
Appusage    1.0
 
aragorn   1.2.36
    
arwpost    2.2
  
ase   3.6.0
 3.7.1
 
The Atomic Simulation Environment (ASE) is the common part of the simulation tools developed at CAMd. ASE provides Python modules for manipulating atoms, analyzing simulations, visualization etc.
asreml  3.0vb
2.00ah
    
ASReml is a statistical software package for fitting linear mixed models using restricted maximum likelihood, a technique commonly used in plant and animal breeding and quantitative genetics as well as other fields. It is notable for its ability to fit very large and complex data sets efficiently, due to its use of the average information algorithm and sparse matrix methods.
ATLAS    3.8.2
 
Automatically Tuned Linear Algebra Software
atp    1.2.1
1.2.0
1.1.3
  
augustus   3.0.2
    
autoconf     2.69
 
AUTODOCK  4.2.3
    
Automated docking of flexible ligands to macromolecules. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AUTODOCK
autodock_vina   1.1.2
    
automake    1.13.1
 
autotools    all
 
barrnap   0.2
    
BayeScan    2.1
 
bcompare    3.1.6
  
beagle   1.0
    
beagle_gpu   1.0
    
beast   1.7.4
1.7.5
    
bedtools   2.17.0
    
berkeley-upc    2.12.1
  
best   2.3.1
    
bioscope    1.2.1-5
 
bismark   0.10.1
    
bison    2.4
  2.6.5
2.3
blacs    1.1.0
 
Basic Linear Algebra Communication Subprograms.
BLAST  2.2.26
  blast-2.2.19
 
Searches a protein or DNA sequence data bank.
blast+   2.2.26
    
blat   3.5
    
blcr    0.7.3
  
bonnie++    1.03e
  
boost  1.53.0
1.48.0
 1.52.0
1.55.0
1.53.0
1.48.0
1.47.0
bowtie   1.0.0
    
bowtie2   2.1.0
2.0.0-beta7
    
bsponmpi    0.3
  
bwa   0.7.5a
    
CaGe    1.0
 
camino    1010
 
cdat    5.2
  
cdbfasta   2003.09.06
    
cdo    1.4.1
1.3.1
1.2.1
1.5.6.1
1.6.0
1.5.6.1
cd_hit   20070131
    
cegma   2.4.010312
    
cfitsio  3.300
  3.25-gnu
  
cfour    1.0-mpi
 
Coupled-Cluster techniques for Computational Chemistry (CFOUR) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Møller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well.
cfx      14.0.0
cgns       3.1.4
chapel    1.3.0
1.2.1
1.1.1
1.2.0
1.6.0
Chapel is a new parallel programming language being developed by Cray Inc.
CLCBioMainWorkBench    7.0
 
CLCGenomicsWorkBench    7.0
 
clearcut   1.0.9
    
clonalorigin   41
    
ClustalW  2.1
2.0.12
    
Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.
ClustalW-MPI    0.13
 
A Parallel Implementation of ClustalW, based on MPI. See also ClustalW.
clustalw2    2.0.10
 
cmake  2.8.9
2.8.7
2.6.4
2.4.8
2.8.9
2.8.8
2.8.11.2
Coin3D    3.0.0
 
COMSOL      4.3b
Multiphysics simulation software.
copygb    2008-12
  
coreutils    0.0
  
cp2k  2.3
    2.5.1
2.4
CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
CPLEX    123
 
High-performance software for mathematical programming and optimization.
CPMD    3.13.2
  3.17.1
The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
CrayPat    5.1.3
5.1.2
5.0.1
  
Cray Performance Analysis Tool. Evaluates program execution on Cray systems.
cuda  5.5.test
5.0
5.5
  5.5
 
CUDA is NVIDIA\'s parallel computing architecture.
cufflinks   2.1.1
    
cunit    2.1-0
  
curl    7.19.5
  7.19.7
dacapo    07022011svn
 
DACAPO is an ab initio molecular dynamics code, based on ultra-soft pseudopotentials.
Dalton    DALTON2011
2013.2
Dalton QCP (Quantum Chemistry Program) represents a powerful quantum chemistry program for the calculation of molecular properties.
ddt       4.2
defuse   0.6.1
    
Denoiser   0.91
    
diesel    1.16.1
 
Dirac    10
 
Program for atomic and molecular Direct Iterative Relativistic All-electronic Calculations.
discus   111126
111126.larger_limits
    
dl_poly       4.05
4.04
Dragon    6.0.18
 
ECLIPSE  2011.2
    
Petroleum reservoir simulation.
eigen   3.0.3
 3.1.1
 
elmer       7.2
elph    1.0.1
 
EMBOSS  6.5.7
    
Package for seqence analysis. Tools for molecular biology
EPD    7.3
 
espresso   5.0.2_beef
5.0.1
    4.3.2
ESPRSSO    5.1.0
 
ESyS-Particle    2.3
 
esysparticle   2.2.2_patch
2.1
2.2.2
    
exonerate   2.2.0
    
expat  2.1.0
  2.0.1
  2.0.1
Fasta    1.0
36.3.4
 
Searches a protein or DNA sequence data bank.
fastqc   0.10.1
    
fasttree   2.1.5
    
fastx-toolkit   0.0.13
    
fatotwobit   16122013
    
fcgene   1.0.5
    
ferret    6.6.1-dynamic
6.2-dynamic
6.8.5
 
ffmpeg       0.10
FFTW  3.3.3
2.1.5
3.3.3.mpi
3.3.3
3.3
2.1.5
3.2.2.1
3.2.2
3.2.1
2.1.5.2
3.3.2
3.3.4
3.3
3.3.3
2.1.5
FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of both real and complex data, and of arbitrary input size.
flex       2.5.35
FLUENT      14.0.0
Computational Fluid Dynamics software.
freesurfer  5.3.0
5.1.0
  5.1.0
 
FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.
FSL  4.1.9
4.1.7
  4.1.2
 
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
FVCOM    3.1
 
g95    0.93-32b
0.93
  
A free, open source Fortran 95/2003 compiler and runtime libraries.
galaxy-python   1.0
    
galaxy-R   1.0
    
galaxy-scripts   1.0
    
GAMESS  2013_R1
    
GAMESS (General Atomic and Molecular Electronic Structure System) is a general ab initio quantum chemistry package.
gamessplus   2010.2
    
garli   2.0
    
gasnet       1.20.0
gatk   2.7_4
2.8-1
3.1.1
    
gaussian   g09d01
g09b01
g09c01
g03d02
    
Gaussian 09    09.c01
 
gcc  4.8.0
4.8.2
4.7.2
4.6.2
4.6.0
4.5.3
4.5.2
4.5.1
4.5.0
4.4.4
4.4.3
4.3.3
4.2.4
4.1.2
3.3.3
  4.8.2
4.7.1
4.3
gdal   1.9.1
    
gdb    7.2
  7.3
geneid   1.4.4
    
genemark-es   2.3e
    
genemarks   19032014
    
GenGeo    1.0
 
geodict    2010R1
 
geos  3.3.5
  3.3.0
  
geotiff    1.2.5
  
gfs    080130
 
ggobi    2.1.8
 
ghc   7.4.2
    
GIMIC    2.1.4
 
git    1.6.3.1
1.8.3.4
1.7.10.4
1.6.0.2
glimmer    3.02
 
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
gmap   2013-11-27
2013-09-30
    
GMAP/GSNAP    2012.07.20
 
gmt     4.5.6
 
GNU Compilers    4.4.6
 
gnuplot  4.6.0
4.6.3
  4.4.2
4.2.5
  4.2.3
Gnuplot is a portable command-line driven graphing utility.
gnu_parallel   20131022
    
gold   2.2.0.4
2.1.10.0
  
google-perftools    1.6.0
 
GotoBLAS    1.22
 
Fast implementation of the Basic Linear Algebra Subroutines.
gpaw    0.7.2
 
Density functional theory. GPAW is an efficient program package for electronic structure calculations. It is based on the density-functional theory implemented within the projector augmented wave (PAW) method using uniform real-space grids. GPAW can be used for systems containing up to hundres of atoms and thousands of electrons.
Grace    5
 
GrADS    2.0.a9.oga.1
2.0.a8
1.9b4-gnu
  
The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. The format of the data may be either binary, GRIB, NetCDF, or HDF-SDS (Scientific Data Sets).
graphviz   2.28.0
    
grib       1.9.16
1.11.0
1.10.4
grib-api    1.7.0
  
GRIB API    1.9.16
 
GROMACS   4.6.3.mpi
4.5.5
 4.6.1
4.5.5
4.6.2
Package for molecular dynamics. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS
GSL  1.15
  1.11
1.14
1.16
1.15
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
GTS    071220
 
The GNU Triangulated Surface Library. http://gts.sourceforge.net/
h4toh5    2.1
  
Haskell platform    7.0.4
 
HDF5  1.8.9_pgi
1.8.9_intel
1.8.9
1.8.12_intel
1.8.12
1.8.8
1.8.5.0
1.8.4.1
1.8.3.1
1.6.7a
1.8.9
1.8.9
1.8.9
1.8.7
1.8.12
1.8.11
HDF5 is a data model, library, and file format for storing and managing data.
hdf5-parallel    1.8.5.0
1.8.4.1
1.8.3.1
1.6.7a
  
helloabel   1.0
    
High Performance Networ SSH    5.1p1-hpn13v5
 
HMMER  3.0
3.1b1
  hmmer-2.3.2
 
Profile hidden Markov models. HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. Basically, you give HMMER a multiple sequence alignment as input; it builds a statistical model called a \"hidden Markov model\" which you can then use as a query into a sequence database to find (and/or align) additional homologues of the sequence family. HMMER
hpctoolkit    5.3.2
 
hpczip   7.1
    
hpnssh    5.8p1
  
htslib   121113
    
hwloc       1.4.2
hypre       2.8.0b
ICM-Pro    3.8.1
 
icu   49.1.2
    
idl    8.0
 
imagemagick  6.7.9-0
  6.5.0-10
  
infernal   1.0.2
1.1
    
inspector       13.1
intel  2013.sp1.2
2013.sp1.1
2013.sp1
2013.5
2013.3
2013.2
2013.0
2011.10
13.1
12.1.0
12.0.4.191
12.0.3.174
12.0.2.137
12.0.0.084
11.1.073
  
intel-mkl    11.0.1
10.3.6
   
Intel Advisor XE 2013    2013.4
 
Intel Cluster Studio XE2013    13.0
 
Intel compilers      14.0.1
13.0.1
12.0.5.220
Intel® Compilers help Linux* software run at top speeds. Using Intel Compilers for Linux, developers can write high-performance software for desktops and servers. These compilers are compatible with existing development environments on Linux, so it's easy to start using them. Intel compilers
Intel Inspector XE 2013    2013.4
 
Intel Math Kernel Library    11.0.0
 
Intel MPI    4.1.1
4.0.2
 
intelmpi.gnu   4.1.1
4.0u3
    
intelmpi.intel   4.1.1
4.0u3
    
Intel Performance Analysis tools    2013.1
 
Intel TraceAnalyzer    8.1
 
Intel VTune Amplifier XE    2013.4
 
iobuf    2.0.2
2.0.1
  
ior    2.10.2
  
iozone    3.323
  
iperf    2.0.4
  2.0.5
ipm    0.982
0.982
2.0.2
ipython   1.1.0
    
itk    3.8.0
 
jags   3.3.0
    
jasper  1.900.1
  1.900.1
  
java    jdk1.6.0_24
1.6.0_10
1.7.0_01
lamarc   2.1.8
    
lammps   2013.08.16
  130816
130711
130111
lapack  2013.5
    
Linear Algebra PACKage. A software library for numerical linear algebra. It provides routines for solving systems of linear equations and linear least squares, eigenvalue problems, and singular value decomposition. It also includes routines to implement the associated matrix factorizations such as LU, QR, Cholesky and Schur decomposition. LAPACK was originally written in FORTRAN 77 and is now written in Fortran 90. The routines handle both real and complex matrices in both single and double precision.
lastz   1.02.00
    
libcsoap    1.1.0-16
  
libdap    3.9.3
3.8.2
  
libfast    1.0.9
1.0.8
1.0.7
  
libnc-dap    3.7.3
  
libtool    2.2.6a
 
libxml2    2.6.32
  
lsm    1.0.beta1
 
m4    1.4.16
  1.4.16
1.4.12
macs   1.4.2
    
mafft  6.903
    
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.
maker   2.31
    
map       4.2
materialsstudio   7.0
6.0
5.5
    
Mathematica    8.0.4
 
Matlab  R2012a
  2009a
2008b
2007b
R2010b
R2013b
R2013a
MATLAB is a language for technical computing that combines numeric computation, advanced graphics and visualization, and a high-level programming language. It is the natural environment for analysis, algorithm prototyping and application development. MatLab
matlab-mcr   R2012b
R2012a
    
matlab-nag   23.0
    
maxwell       14.0
mcmcphase   2.0
    
mdynamix       5.2.4
MEME    4.4.0-intel
4.4.0-gnu
  
mercurial       2.0
mesalib    7.4.4
  
mgltools   1.5.4
    
microbiomeutil   20110519
    
MIGRATE   3.3.2
    
mira   4.0rc4
3.4.0
    
mkl      12.0.5.220
mmtsb    1.0
 
Multiscale Modeling Tools for Structural Biology.
moab    6.0.2-s1407
  
Modules    3.1.6.6
  
Provides dynamic modification of a user's environment via modulefiles.
molcas    7.8
 
MOLCAS is an ab initio computational chemistry program, developed at Lund University in collaboration with others. Focus in the program is placed on methods for calculating general electronic structures in molecular systems in both ground and excited states. MOLCAS is, in particular, designed to study the potential surfaces of excited states.
Molden  5.0.4
5.0.4
 5.0.4
 
Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.
molpro  2012.1.p0
2012.1.0
  2012.1.0
 
Molpro quantum chemistry package.
mothur   1.31.2
1.26.0
    
MoViPac    1.0.0
 
mpe2    1.1.1
  
mpiBLAST    1.5.0-pio
1.6.0
Searches a protein or DNA sequence data bank. BLAST
Mpiexec    0.83
 
Mpiexec is a replacement program for the script mpirun, which is part of the mpich package. It is used to initialize a parallel job from within a PBS batch or interactive environment. Mpiexec
mpt       2.09
2.06
2.05
MrBayes  3.2.1
    
Program for the Bayesian inference of phylogeny. MrBayes
mrbayes_gpu   2.1.1
    
mrmodeltest   0.2
    
mrnet    3.0.0
2.2.0.1
2.0.1.1
  
Multiphysics    4.3b
 
mummer   3.23
    
mumps    4.9.2
4.10.0
MUMPS: a parallel sparse direct solver.
muscle   3.8.31
    
mvapich2    1.2p1
 
NAMD  2.9
2.9.0
2.8b1
2.8
2.9.mpi
2.9
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
nbo   6.0
    
NBO6    6.0
 
nccmp    1.4.0
 
NCIplot    3.0
 
ncl   6.1.0
2.1.18
    6.1.2
ncl_ncarg    5.2.0-login
5.2.0
5.1.1-login
5.1.1
  
NCO  4.3.4
  4.0.7-login
4.0.5
4.0.0
3.9.6
4.3.6
4.3.1
4.1.0
The netCDF Operators, or NCO, are a suite of programs known as operators. The operators take netCDF files as input, then perform a set of operations (e.g., deriving new data, averaging, hyperslabbing, or metadata manipulation) and produce a netCDF file as output.NCO
ncview  2.1.2
  2.0beta4
1.93g
  2.1.2
Ncview is a visual browser for netCDF format files.ncview
nedit    5.5
  
NetCDF  4.2.1.1
4.1.3
4.1.1.0
4.0.1.3
4.0.1.1
3.6.2
4.1.3
4.2.1.1
4.3.1
4.3.0
4.1.3
3.6.2
NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data.NetCDF
NetCDF-4 viewer    2.1.2
 
netcdf-hdf5parallel    4.1.1.0
4.0.1.3
4.0.1.1
  
netcdf.gnu   4.2.1.1
    
netcdf.intel   4.2.1.1
    
netcdf.pgi   4.2.1.1
    
Netlib    1.8.0
 
newbler  2.9
2.8
2.7
2.6
2.5.3
2.3
1.1.03.24
2.0.01.02
    
Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Sciences, a Roche Diagnostics company.
nfuse   0.2.1
    
nltk   2.0.1
    
notur   0.1
  default
v0.3~
v0.3
NWchem    6.0-python
6.0-dynamic
5.1.1
6.1
6.3
NWchem is a computational chemistry package which provides many methods to compute the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density.
ocaml   4.00.0
    
Octave  3.6.3
    3.6.4
GNU Octave is a high-level language, primarily intended for numerical computations.
octopus    3.2.0
 
open64   5.0
    
openbabel    2.2.0
 
Open Babel: The Open Source Chemistry Toolbox.
opencl       1.2-3.0.67279
openfoam    1.7.1-dso
1.7.1
1.6
1.5
2.1.0
2.3.0
2.2.2
2.2.0
The open source CFD toolbox.
openjpeg       2.0.0
1.5.0
OpenMPI   1.6.4
1.6.3
1.4.4-gnu
1.4.4
 1.6.2
 
Open MPI is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. A completely new MPI-2 compliant implementation.OpenMPI
openmpi.gnu   1.7.5
1.8
1.7.4
1.7.3
1.7.2
1.6.1
1.6.3
1.7
1.6.5
1.6.4
    
openmpi.gnu-ilp64   1.6.4
    
openmpi.intel   1.8
1.7.5
1.7.4
1.7.3
1.7.2
1.7
1.6.5
1.6.4
1.6.3
1.6.1
    
openmpi.open64   1.7.2
1.7
1.6.4
1.6.3
1.6.1
    
openmpi.pgi   1.7.5
1.7.4
1.7.2
1.7
1.6.5
1.6.4
1.6.3
1.6.1
    
openspeedshop       2.0.2-u6
openssl       0.9.8j
orca    2.9.1
 
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
paml   4.6
    
pandaseq   2.6
    
papi   5.3.0
  4.1.2
5.2.0
5.2.0
5.1.0
4.4.0
paraview  3.98.0
  3.6.1
  3.14.1
4.0.1
ParaView is an open-source, multi-platform data analysis and visualization application.
Paraview server    3.10.1
 
parmetis    3.1.1
4.0.2
Parallel MeTiS. Parallel Graph Partitioning and Fill-reducing Matrix Ordering
parsinsert   1.04
    
pathscale    3.2.99
  
PAUP  4b10
    
Tools for inferring and interpreting phylogenetic trees.PAUP
pblat   1.0
    
pbzip2   1.1.6
    
pcl       1.7.0
pcre   8.31
    
Perl    5.8.8-dyn
  5.10.0
Scripting language of choice for most CGI scripts. Perl
perlmodules   5.10_2
5.10_1
    
PETSc    3.1.08
3.1.05
3.1.04
3.0.0.10
2.3.3a
petsc-3.1-p2
3.4.1z
3.4.1s
3.4.1d
3.3-p2z
3.3-p2s
3.3-p2d
PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for all message-passing communication.PETSc
petsc-complex    3.1.08
3.1.05
3.1.04
3.0.0.10
2.3.3a
  
pgi  14.3
14.2
14.1
13.9
13.7
13.6
13.5
13.4
13.3
13.2
11.10
  9.0.4
8.0.6
7.2.5
7.1.6
11.6.0
11.5.0
11.4.0
10.9.0
10.8.0
10.5.0
  
phonopy   1.8.1
1.7.1
    
Phylip    3.68
 
PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. Phylip
phylobayes  3.3e
3.3d
    
PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers (e.g. MrBayes), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. It is particularly well suited for large multigene alignments, such as those used in phylogenomics.
phyml  3.0
20120412
    
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
picard-tools   1.107
1.102
    
pkgconfig    0.15.0
  
plink   1.07
    
ploticus       2.42
pnetcdf    1.1.0
  1.3.1
pplacer   1.1
    
prodigal   2.60
    
proj    4.6.1
  4.8.0
4.7.0
prokka   1.7
    
ProMax     5000.0.3.0
 
protobuf   2.4.1
    
prottest   3.2
    
Psi    psi3
 
Python   3.3.0
2.7.2
2.7.1-dso
2.6.5-dynamic-exper
2.6.2
2.7.3
2.7.6
2.7.3
2.7.2
2.6.8
Python, an interpreted, interactive, object-oriented, extensible programming language. Link to a tutorial. Python
python2   2.7.3
    
python3   3.2.3
    
qiime   1.8.0
1.5.0
  1.8.0
 
qt    4.4.3
 
R  2.15.2
2.15.2.shlib
3.0.1
3.0.1.shlib
3.0.2
3.0.2.profmem
3.0.2.shlib
3.0.3
3.0.3.profmem
3.0.3.shlib
  2.11.1
2.15.2
3.0.1
2.15.2
R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files.
Randlib    90
 
RAxML  7.3.1
7.4.2
7.7.6
7.7.6.dontuseme
7.7.6_openmpi
7.8.3
    
RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.
repeatmasker   4.0.5
    
Resource Accounting Service    2.1.5.0
 
rip4    4.6
  
rtax   0.981
    
Ruby      1.8.7.p357
Ruby is a dynamic, reflective, general purpose object-oriented programming language.
sac     101.3b
 
samtools   0.1.18
0.1.19
    
sas    9.2
 
scalapack    2.0.2
 
scalasca   1.4.2
1.4.3
2.0
    1.4.2
schrodinger    2014.1
 
Schrodinger Suite.
schroedinger    2012.04.05
 
Schrodinger Suite.
SCons    2.1.0
 
siesta   3.1
    
silo       4.9.1
smrtanalysis   2.1.1
1.3.0
1.3.1
1.3.3
1.4.0
2.0.1
2.1.0
2.1.0_beta
    
snap   20131129
    
snoseekerngs   1.0
    
soapdenovo2   r223
    
sparsehash    1.8.1
  
sprng   4.4
    
starccm+       8.02.008
9.02.005
stat    1.1.3
1.1.2
1.1.1
  
stata  12
13
11
  12
 
structure  2.3.3
  2.3.4
 
Subversion    1.6.2
  1.5.7
Subversion version control system clients
SuiteSparse    4.0.2
 
svn     1.7.7
 
swig   2.0.11
2.0.11_intel
  2.0.7
 
SYMBIOSES    0.9
 
system manual pages    1.0
 
syzygy   1.2.8
    
taskfarm   1.0
    
tau       2.22.2
tbl2asn   2013.09.23
    
tcl    8.5.8
  8.5.5
tinker    6.3.3
 
The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
tools    lmt-gui
  
tophat   2.0.9
    
torque    2.4.14
  
TotalView  8.9.2.1
8.13.0.0
8.12.0.1
  8.9.1
8.9.0
8.8.0a
8.7.0
8.6.0
8.12.0-0
8.13.0-0
8.12.0-1
TotalView, a source- and machine-level debugger with support for Fortran, C, C++, OpenMP, MPI, and threads. TotalView
tpsl    1.1.00
1.0.01
1.0.0
  
trackvis    0.5.1
 
treefinder   march2011
    
trilinos    10.6.2.0
10.6.0
10.2.0
10.0.1
  11.2.4
trim-galore   0.3.3
    
Turbomole  6.5
  6.4-mpi
 
Program Package for ab initio Electronic Structure Calculations.
uclust   1.2.22
    
ucsc-tools   2014-01-21
    
udunits    2.1.7
  2.2.4
2.1.24
umcp    11
 
UNPHASED  3.0.10
3.1.6
    
Software for genetic association analysis.
usearch   5.2.32
    
valgrind  3.8.1
3.8.1
3.7.0
 3.8.1
3.7.0
Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.
vasp  5.2.11
5.3.2
5.3.3
5.3.3bfix
5.3.5
  5.3.3
5.3.3
5.3.5
Vienna Ab-initio Simulation Package.
vcftools   0.1.12a
    
velvet   1.2.10
1.2.07
  1.2.08
 
viennarna   2.0.7
    
vim    7.2
7.4
7.2
visit     2.4.2
2.6.3
vislcg3   2012.09.27
    
vmd   1.9.1
 vmd-1.9.1
 
vtk       6.0.0
5.8.0
VTK - Visualization Tool Kit    5.10.1
 
vtune      13.1
vtune_amplifier   2013.3
    
wise2   2.4.1
    
wps    3.3.1
3.3
3.2.1
3.2
3.1.1
3.1
3.0.1
  
wrf    clWRF
3.3.1
3.3
3.2-mpt4
3.2.1
3.2
3.1.1
3.1
3.0.1.1
2.2.1
  
wrfchem    3.2.1
3.2
3.1.1
3.1
3.0.1.1
  
wrfda    3.2
3.1.1
  
wrfnl    3.2
  
wrfplus    3.2
  
wrfpolar    3.1.1
  
xmakemol    5.16
 
XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds.
xmgrace   5.1.23
    
xt-asyncpe    5.00
4.9
4.8
4.7
4.6
4.5
4.4
4.3
4.2
4.0
3.9
3.4
  
xt-lgdb    1.4
1.3
1.2
  
XT-libsci    10.5.02
10.5.01
10.5.0
10.4.9
10.4.8
10.4.5
  
Cray Scientific Library that includes optimized LAPACK, BLAS, BLACS, ScaLAPACK, SuperLU, IRT
xt-mpt    5.3.1
5.3.0
5.2.3
5.2.2
5.2.1
5.2.0
5.1.4
5.1.3
5.1.2
5.1.1
5.1.0
5.0.2
5.0.1
5.0.0
4.1.1
4.1.0.1
4.0.3
4.0.2
4.0.1
4.0.0
3.5.1
3.4.2
3.3.0
3.2.0
  
xt-papi    4.1.2
4.1.0.0.2
4.1.0
3.6.2.2
3.6.1a
  
yaml   0.1.4
    
zeromq   3.2.4