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 on the left 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The table represents the current situation fairly accurately, but may contain incomplete or out-of-date entries.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

		gardar	hexagon	njord	stallo	titan	vilje
454apps						2.6 2.5.3 2.3 2.0.01.12 1.1.03.24
abaqus				6.9-2 6.10-4 6.7-EF1
A suite of software applications for finite element analysis.
abyss			1.2.3 1.2.1			1.3.2 1.3.1
ACESII						mab_2005.1
ACES II is a set of programs that performs ab initio quantum chemistry calculations. ACES II was written and is maintained in Rod Bartlett\'s research group. It implements the Coupled Cluster and Many Body Perturbation Theory methods that were developed over many years by Bartlett and his collaborators.
ACML			4.4.0 4.3.0 4.2.0	N.A.
AMD Core Math Library
acml.gfortran						4.4.0 4.1.0 3.6.0
AMD Core Math Library
acml.gnu						4.1.0 3.6.0
AMD Core Math Library
acml.ifort						4.4.0 4.3.0 4.2.0 4.1.0 3.6.0
AMD Core Math Library
acml.pathscale						4.1.0 3.6.0
AMD Core Math Library
acml.pgi						4.1.0 3.6.0
AMD Core Math Library
ADF				2012.01 2010.02c 2010.02b 2010.02 2009.01-23077 2009.01a 2009.01b 2008.01	Development.snapshots 2010.snapshot 2010.02b 2010.01.snapshots 2010.01 2009.01.snapshots 2009.01 2008.01 2007.01	2010.02b 2010.02 2009.01 2008.01
ADF is the Amsterdam Density Functional program system for electronic structure calculations.
admb						10.0
alglib					3.0
ALGLIB is a cross-platform numerical analysis and data processing library.
AMBER				9.0.35	9.0.35 11 10
A package of molecular simulation programs.
AmpliconNoise						1.24 1.21
AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons.
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
arwpost			2.2
ase					3.4.1_py2.5 3.4.1
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						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						2.5.5
autoconf						2.68
bcompare			3.1.6
beast						1.6.1 1.5.4
bedtools						2.7.1
berkeley-upc			2.12.1	xlupc
best						2.3.1
biogrid						muscle mafft hmmer clustalw blast+ blast 1.00+ 1.00
bioscope					1.2.1-5
bison			2.4
blacs					1.1.0
Basic Linear Algebra Communication Subprograms.
BLAST					blast-2.2.19 blast-2.2.18	2.2.25 2.2.18
Searches a protein or DNA sequence data bank.
blast+						2.2.25
blat						3.4
blcr			0.7.3			0.6.1
blitz				0.9		0.9
Blitz++ is a C++ class library for scientific computing which provides performance on par with Fortran 77/90. It uses template techniques to achieve high performance. The current versions provide dense arrays and vectors, random number generators, and small vectors and matrices.
bonnie++			1.03e
boost				1.47.0 1.40.0	1.46.1 1.42.0	1.48.0
breve						2.7 2.4.1
A 3d Simulation Environment for Multi-Agent Simulations and Artificial Life
bsponmpi			0.3
CaGe					1.0
camino					2.880
cdat			5.2
cdbfasta						0.99
cdo			1.4.1 1.3.1 1.2.1
cegma						2.4
celera						6.1
cfitsio			3.25-gnu			3.24
cfour					rc1.0_mpi rc1.0
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				13.0.0
chapel			1.3.0 1.2.1 1.1.1	1.1.1 1.0 0.9	1.2.0
Chapel is a new parallel programming language being developed by Cray Inc.
cilk						5.4.6
clonalorigin						15.02.2011
ClustalW					2.0.10	2.0.9
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.
cmake			2.6.4 2.4.8	2.6.4 2.8.0-rc5	2.6.2 2.8.2	2.8.5 2.6.4
cmiss						x.x.0
cmkl						8.1
Coin3D					3.0.0
compython						bak.2.1 2.5.openmpi 2.5 2.3 2.1
COMSOL					4.2 4.1 3.5 3.4
Multiphysics simulation software.
configobj						4.7.2
copygb			2008-12
coreutils			0.0	7.2
cp2k					2.0	8.12.2011 31.03.2011
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					121
High-performance software for mathematical programming and optimization.
CPMD			3.13.2	3.13.2 3.11.1
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	N.A.
Cray Performance Analysis Tool. Evaluates program execution on Cray systems.
cuda					3.2.16	4.0.17
CUDA is NVIDIA\'s parallel computing architecture.
cunit			2.1-0
curl			7.19.5
dacapo					07022011svn
DACAPO is an ab initio molecular dynamics code, based on ultra-soft pseudopotentials.
Dalton				2.0 cvs	r9829 r9029_largemolecules r9029 r10173 mcscf-j 2.0	2011
Dalton QCP (Quantum Chemistry Program) represents a powerful quantum chemistry program for the calculation of molecular properties.
delph-in						intel-mkl-last intel-mkl intel-goto2-last intel-goto2 intel-atlas-last intel-acml-last intel-acml intel gnu-goto gnu-acml gnu gcc-mkl-last gcc-goto2-last gcc-atlas-last gcc-acml-last 1.00
Denoiser						0.91
Dirac					r14231 r13928 r13871 r13692 10
Program for atomic and molecular Direct Iterative Relativistic All-electronic Calculations.
dmtcp						1.2.3
dxa				1.2.5
ECLIPSE						2009.2 2011.2
Petroleum reservoir simulation.
eigen					3.0.0 2.0.15
elph					1.0.1
EMBOSS						6.4.0 4.1.0
Package for seqence analysis. Tools for molecular biology
ePCR						svn
espresso						4.2.1
ESSL				4.4.0.0
IBM core math library ESSL
exonerate						2.2.0
expat			2.0.1	2.0.1
Fasta					36.3.4 35.4.7
Searches a protein or DNA sequence data bank.
fastx						0.0.10
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
ferret			6.6.1-dynamic 6.2-dynamic
ffmpeg						0.5
FFTW			3.2.2.1 3.2.2 3.2.1 2.1.5.2	3.2.2 2.1.5 3.1.2	2.1.5 3.1.2 3.2.2	3.2.2.intel 3.2.2.gnu
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
fltk				1.1.8 1.1.9 1.1.7
FLUENT				13.0.0
Computational Fluid Dynamics software.
freesurfer					5.1.0 4.2.0 4.0.4
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					4.1.6 4.1.4 4.1.2 4.0.4_64 4.0.2	4.1.7 4.1.2
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
ftgl				2.1.3-rc5
g03				d01 c02	e01	d02
Gaussian 03
g09					b01	b01
Gaussian 09.
g95			0.93-32b 0.93			093
A free, open source Fortran 95/2003 compiler and runtime libraries.
gamessplus						v2010
garli						1.0 0.94
gcc			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	4.4.5		4.6.1 4.6 4.5.1
gdb			7.2
gdl						0.9rc4 0.9rc2 0.9
geneid						1.4.4
geodict					2010R1
geos			3.3.0
geotiff			1.2.5
gfs					080130
ggobi					2.1.8
ghc						6.12.3
git			1.6.3.1		1.7.1	1.7.6.4
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.
gmt					4.5.6
gnuplot			4.4.2 4.2.5	4.4.3		4.4.2 4.2.5
Gnuplot is a portable command-line driven graphing utility.
gold			2.1.10.0		2.1.5.0
google-perftools					1.6.0
google-test					1.5.0_gcc 1.5.0
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.
GPFS				3.1.0.27
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						2.6 2.24.0 2.20.2
grasp				4.0
grib-api			1.7.0
GROMACS				4.5 4.0.5 3.3.3	4.0.5 3.3.3	4.5.3
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			1.11	1.13 1.12	1.14 1.12	1.9 1.8.32b 1.15 1.13 1.12
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
gtest					1.5.0_gcc 1.5.0
GTS					071220 0.7.6
The GNU Triangulated Surface Library. http://gts.sourceforge.net/
h4toh5			2.1
h5py						1.3.0
HDF5			1.8.5.0 1.8.4.1 1.8.3.1 1.6.7a	5-1.8.5p1 5-1.6.5 5-1.6.10		1.8.4.patch1 1.8.7 1.8.1
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
hdf5.pic						1.8.1
hdfview						2.5
HDFView is a visual tool for browsing and editing HDF4 and HDF5 files.
HMMER					hmmer-3.0rc2	2.3.2 3.0
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					1520
hpn-ssh					5.1p1-hpn13v5
High Performance SSH/SCP
hpnssh			5.8p1	5.8p1-13v11
ibmpich						1.0
icu						4.8.1.1
idl					8.0 6.4
IHPCT				2.2.2
IBM High Performance Computing Toolkit
ima2						4.11.11
imagemagick			6.5.0-10			6.7.2.5 6.5.3.3
instant						0.9.5 0.9.4
intel			12.0.4.191 12.0.3.174 12.0.2.137 12.0.0.084 11.1.073			9.1 2011.8 2011.3 2011.1 11.1u8 11.1u7 11.1 11.0 10.1
intel-mkl					2011.4.191 10.2.0.013 10.1.0.015
intel-mpi					4.0.1.007
intel-tools					XE2011
Intel compilers					12.0.4 11.1_ia32 11.1.072 11.1 11.0 10.1 10.0
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
intellib						9.1 11.0 11.1 10.1
iobuf			2.0.2 2.0.1
ior			2.10.2
iozone			3.323	3.347
iperf			2.0.4	2.0.4
ipm			0.982	0.982 0.922	0.982	0.983 0.982b 0.982
itk					3.8.0
jags						1.0.3 2.2.0
jasper			1.900.1	1.900.1
java			jdk1.6.0_24	1.5.0	1.6.0_10
jellyfish						1.1.2
lamarc						2.1.6
lammps				110505 110505-2 110104 101207-ersland
lammps-icms				110304-omp 110304
Landmark					LSM5000.0.3.1
lapack				3.3.1 3.0.20021004
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.
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				1.5.8	2.2.6a
libxml2			2.6.32	2.7.7
libxslt				1.1.26
LoadLeveler				3.5.0.5
LoadLeveler is the workload manager on the Regatta. CXperf
local						1.0.0.b0rk 1.0.0
lsdyna				9.7.1.r421 9.7.1
lsm					1.0.beta1
m4			1.4.16
mafft						6.851 6.833 6.811 6.603
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.
maker						2.1
Matlab			2009a 2008b 2007b	N.A.	R2010b R2009a 2007b	R2010b R2008b 7.7
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
mdynamix				5.1
meltprofile						1.0
MEME			4.4.0-intel 4.4.0-gnu			4.6.0
mesalib			7.4.4			7.6.1
mga					1.0
microbiomeutil						2011.05.19 2010.12.12
MIGRATE						3.2.9
mira						3.4.0 3.2.1 3.0.5
mkl					2011.4.191 10.1.0.015 10.2.0.013
mmtsb					1.0
Multiscale Modeling Tools for Structural Biology.
moab			6.0.2-s1407
Modules			3.1.6.6	3.2.7
Provides dynamic modification of a user's environment via modulefiles.
molcas					7.4
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					4.9 4.8 4.6
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						2010.1.p3 2008.1 2010.1
Molpro quantum chemistry package.
mothur						1.23.1 1.22.2
mothur_mpi						1.23.1 1.22.2
mpe2			1.1.1
MPI				poe
MPI (Message Passing Library) is a widely used standard for writing message-passing programs. The interface attempts to establish a practical, portable, efficient, and flexible standard for message passing. MPI
mpiBLAST				1.6.0.b1	1.5.0-pio	1.6.0
Searches a protein or DNA sequence data bank. BLAST
Mpiexec					0.83 0.82
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
mrnet			3.0.0 2.2.0.1 2.0.1.1
mtag						1.0
mumps					4.9.2
MUMPS: a parallel sparse direct solver.
muscle						3.7
mv++				1.5
mvapich2					1.2p1
NAMD			2.8b1 2.8	2.7 2.6	2.7b1 2.6-TCP 2.6
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NCARG				4.4.0 5.0.0
NCAR Graphics
ncbi_blast						2.2.25+
ncl_ncarg			5.2.0-login 5.2.0 5.1.1-login 5.1.1
NCO			4.0.7-login 4.0.5 4.0.0 3.9.6	3.9.1 3.1.8	4.0.5
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			2.0beta4 1.93g
Ncview is a visual browser for netCDF format files.ncview
nedit			5.5	5.5
NetCDF			4.1.1.0 4.0.1.3 4.0.1.1 3.6.2	4.1.1 3.6.3_u 3.6.2 3.6.1	4.1.1 3.6.2	4.1.1 4.0.1.intel
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-hdf5parallel			4.1.1.0 4.0.1.3 4.0.1.1
netcdf.g77						3.6.2
netcdf.gfortran4						3.6.2
netcdf.intel						3.6.2
netcdf.pathscale						3.6.2
netcdf.pgi						3.6.2
Netlib					1.8.0
netpbm				10.26.44
newbler						2.6 2.5.3 1.1.03.24 2.0.01.12 2.3
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.
Newmat				10d
Newran				02c
Newran is a C++ library for generating sequences of random numbers from a wide variety of distributions.
numpy				1.5.1rc2 1.2.1		1.6.1 1.6.0b2 1.5.1rc1 1.4.1
NWchem			6.0-python 6.0-dynamic 5.1.1
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						3.11.1
Octave						3.4.0
GNU Octave is a high-level language, primarily intended for numerical computations.
octopus					3.2.0
ode						0.11.1 0.11.1s
open64						5.0 4.2.3 4.2.1
openbabel					2.2.0
Open Babel: The Open Source Chemistry Toolbox.
openbugs						3.2.1
BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. The user specifies a statistical model, of (almost) arbitrary complexity, by simply stating the relationships between related variables. The software includes an ‘expert system’, which determines an appropriate MCMC (Markov chain Monte Carlo) scheme (based on the Gibbs sampler) for analysing the specified model. The user then controls the execution of the scheme and is free to choose from a wide range of output types.
openfoam			1.7.1-dso 1.7.1 1.6 1.5	1.6.101022 1.7.1 1.6.100210 1.5.100224-dev 1.5.090616 1.5.090915-dev	1.7.1 1.6.100222 1.6.091030 1.6
The open source CFD toolbox.
OpenMPI				poe	1.4 1.3.3_gfortran44 1.3.3_gfortran 1.3.3_10.1 1.3.3 1.3.2_nodso 1.3.2 1.2.8 1.2.4	1.4.intel.icc 1.4.intel 1.4.3.pgi 1.4.3.open64 1.4.3.intel.test 1.4.3.intel 1.4.3.gnu32 1.4.3.gnu 1.4.2.intel 1.3.3.pgi 1.4.1.intel 1.4.1.gnu 1.3.3.intel.ipath 1.3.3.intel 1.3.3.gnu 1.2.8.intel 1.2.8.gnu
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
openssl						1.0.0b
orca					2.6.35
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.
p4vasp					0.3.20	0.3.19
The p4vasp package is a set of tools for processing xml-formatted VASP output (i.e. vasprun.xml files).
papi			4.1.2	4.1.1		4.1.2.1 3.6.2 4.1.0
paralleloctave						x.x.0
paraview			3.6.1			3.6.1 3.4
ParaView is an open-source, multi-platform data analysis and visualization application.
parmetis					3.1.1
Parallel MeTiS. Parallel Graph Partitioning and Fill-reducing Matrix Ordering
pathscale			3.2.99	N.A.		test2 test intel c62b750 3.2 3.0
PBS/Torque				LoadLeveler
PBS Pro (Portable Batch System) is the workload manager on the HP installations. Link to Maui, the advanced job scheduler. Link to OpenPBS. PBS
pbzip2				1.1.1
Perl			5.8.8-dyn	5.8.2.1		1.7 1.6 1.0
Scripting language of choice for most CGI scripts. Perl
PESSL				3.3.0.4
PETSc			3.1.08 3.1.05 3.1.04 3.0.0.10 2.3.3a	3.0.0.11-complex 3.0.0.11-real 3.1.101122-complex 3.1.101122-real 2.3.3.3 2.3.2.8 2.3.2.3	petsc-3.1-p2	3.1-p8
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			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	N.A.		11.10 7.1 11.1 10.9 10.5 10.2
phredphrapconsed						2.0 1.0
The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.
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						3.3b 3.2e 3.2d
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.vector 3.0 2.4.5
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
pigz				2.1.6
pkgconfig			0.15.0	0.23
plink						1.07 1.06 1.05
ploticus				2.41
plotmtv				1.4.1
plplot						5.9.4
PMDR				1.0
Parallel Multifactor Dimensionality Reduction
pnetcdf			1.1.0
poe				4.3.2.11
poy						4.1.1
prank						100802
procov						2.0
proj			4.6.1	4.7.0
ProMax					5000.0.3.0
pymol						1.2
pyopenssl				0.11
pyronoise						2
Software for Pyrosequencing Noise Removal
pysundials						2.3.0b6
Python			2.7.1-dso 2.6.5-dynamic-exper 2.6.2	3.1.1 2.6.3 2.5.0	2.7.1 2.6.2_local 2.6.2_intel 2.6.2 2.5.1	3.1.1 2.7.gcc45 2.6.2 2.7
Python, an interpreted, interactive, object-oriented, extensible programming language. Link to a tutorial. Python
qiime						1.3.0 1.2.1
qt				3.3.5	4.4.3	4.3.3
R			2.11.1		2.9.2 2.9.1 2.8.1 2.12.1 2.11.1 2.10.0	2.13.2 2.11.1 2.10.1
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.
r8s						1.71
RAxML						7.0.4 7.2.6
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						3.0
rip4			4.6
rmblast						1.2_ncbi_blast_2.2.23+
root						v5.27.06 v5.24.00
Ruby						1.9.2 1.9.1
Ruby is a dynamic, reflective, general purpose object-oriented programming language.
sac					101.3b
sas					9.2
scalapack					1.8.0
scampi						5.6.1
Scali MPI Connect. Discontinued.
schroedinger					2011.04.19 2010_06_15_mx 2010-10-19_mxd	2011.04.19.old 2011.04.19 2011.03.11
Schrodinger Suite.
scipy						0.8.0 0.7.2
snap						2006.07.28
sparsehash			1.8.1			1.12 1.11
stat			1.1.3 1.1.2 1.1.1
stata					10	11
structure					2.3.1	2.3.3 2.2.3 2.2.2
Subversion			1.6.2	1.6.9 1.4.2 1.4.3
Subversion version control system clients
sundials				2.3.0 2.4.0		2.3.0
svn					1.6.17	1.4.6 1.6.16
tables						2.1.2
tcl			8.5.8	8.4.7
teiresias						01.09.2011
tinker					5.1
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
torque			2.4.14	LoadLeveler
TotalView			8.9.1 8.9.0 8.8.0a 8.7.0 8.6.0	8.6.2-0 8T.6.0-1 8.0.1-0	8.6.1-1 8.6.0-2 8.3.0-1
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
TRE						0.8.0
treefinder						march2011
TRF						4.04
trilinos			10.6.2.0 10.6.0 10.2.0 10.0.1
Turbomole					6.3_serial 6.3_parallel 6.3_felles 6.2_parallel 6.2_huge_serial 6.2_huge_parallel 6.0.2_serial 6.0.2_parallel 5.10_serial 5.10_parallel
Program Package for ab initio Electronic Structure Calculations.
uclust						1.2.22
udunits			2.1.7			2.1.21
umcp					11
UNPHASED						3.0.10 3.0.13
Software for genetic association analysis.
valgrind					3.5.0 3.6.0	3.5.0
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				5.1.39 4.6.28 4.6.31		4.6.36.parallel 5.2.11.parallel 5.2.2.parallel
Vienna Ab-initio Simulation Package.
velvet						1.1.04 1.1.06 1.0.19
vim			7.2	6.3
vislcg3						test5 gprof 1.0 0.9.7.6500
VPA				4.0.0
Visual Performance Analyzer (VPA) is an Eclipse-based performance visualization toolkit.
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
WSMP				7.5.18
Watson Sparse Matrix Package
x10				2.0.6
XLC				11.1.0.4 9.0.0.0
XL C is a standards-based, high performance C compiler with advanced optimizing and debugging features.
XLF				13.1.0.4 11.1.0.0
XL Fortran
xlupc				11.0.0.0
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	ESSL
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	poe
xt-papi			4.1.2 4.1.0.0.2 4.1.0 3.6.2.2 3.6.1a
xz						5.0.0