Alphabetical list of software installed on PSC machines

If you are unfamiliar with the formatting of this list, take a look at this description.

ABINIT, finds the total energy, charge density and electronic structure of systems of electrons and nuclei within DFT using pseudopotentials and a planewave basis.: (BigBen)
ACML, the AMD Core Math Library.: (BigBen, Opteron); (Linux)
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ALIGNACE, scans non-coding nucleic acid sequences at high resolution for motifs that occur with non-random frequency.: (Opteron)
AMBER, uses classical mechanics to study large molecules.: (Pople, Salk, BigBen, Opteron)
ATLAS, Automatically Tuned Linear Algebra Software.: (BigBen)
ATV, a tool for the visualization of annotated phylogenetic trees.: (Opteron)
BLAS, routines for performing vector and matrix operations.: (BigBen, Pople, Salk)
BLASTZ, a multiple sequence alignment program for whole-genome human-mouse alignments.: (Opteron)
CHARMM, mechanics and dynamics of macromolecular systems. Academic and industrial users must make special arrangements for use. See the documentation for details.: (BigBen, Pople, Salk)
CLUSTALW, a package of multiple alignment programs.: (Opteron)
ComAlign, extracts qualitatively good sub alignments from a set of multiple alignments and combines them in a new, often improved alignment.: (Opteron)
CPMD, a parallelized, plane wave/pseudo-potential DFT package, designed for ab-inito molecular mechanics.: (Pople)
DESMOND, a molecular dynamics package.: (BigBen)
DMOVER, scheduled data transfer for distributed computational jobs.: (BigBen)
DRAWP3D, a PSC developed 3D graphics library.: Source code is available.
DReAMM, PSC developed visualization package for MCell models.
EMBOSS, a program suite for nucleic acid and protein sequence analysis.: (Opteron)
FASTA/TFASTA/FASTX/TFASTX, compares a protein or DNA sequence to all of the entries in a sequence library.: (Opteron)
FFTW, a C subroutine library for computing Discrete Fourier Transforms.: (Pople, Salk, BigBen, Warhol)
FLUENT, a fluid dynamics solver which can model fluid flow and heat transfer in complex geometries.: (Pople, Warhol)
FSHIFT, compares a protein query sequence with a translated DNA library sequence.: (Opteron)
GAMESS, an ab initio molecular quantum chemistry program.: (BigBen, Pople)
GAUSSIAN, an ab initio quantum chemistry program. Academic and industrial users must make special arrangements for use. See the documentation for details.: (Pople, Salk, Warhol)
GENBANK, Genetic Sequence Data Bank.: (Opteron)
GENEWISE, compares bio polymers, commonly DNA sequence and protein sequence.: (Opteron)
GNUPLOT, an interactive 2-and 3-D function and data plotting program.: (Pople, Salk, BigBen, Opteron)
GROMACS, molecular dymanics package.: (BigBen, Pople, Salk)
HDF (Hierarchical Data Format), a multi-object file format that facilitates the transfer of various types of scientific data between machines and operating systems.: (Pople, BigBen, Warhol)
HMMER, a software suite for making and using Hidden Markov Models of biological sequences.: (Opteron)
IOBUF, I/O buffering library.: (BigBen)
LAMMPS, a classical molecular dynamics code.: (BigBen)
LS-DYNA, a general purpose transient dynamic finite element program.: (Pople)
LSMS, uses the locally self-consistent multiple scattering method to calculate the electronic structure of large systems within the local density approximation.
m2e, a tool to translate MFIX data files to Ensight 6 data files.: Source code is available.
m2t, a tool to print information from MFIX data files.: Source code is available.
MAFFT, a multiple sequence alignment program for amino acid or nucleotide sequences.: (Opteron)
MakePSSM, creates a Position Specific Scoring Matrix from a multiple sequence file.: (Opteron)
MAKSEQ, helps users create job files to use sequencing packages.: (Opteron)
MAXSEGS, an optimal local sequence alignment program that will find the N-best alignments between two nucleic acid sequences or two protein sequences.: (Opteron)
MCELL, (Monte Carlo Cell), simulates the movements and reaction of molecules within and between cells.: (Salk)
MEME, a set of tools for discovering and using patterns in groups of related sequences.: (Opteron)
MESA, an open source implementation of the OpenGL library.: (Pople)
MFIX, a general program describing hydrodynamics, heat transfer, and chemical reactions in fluid-solids systems. (See also MFIXReader, m2e, m2t, and py2dx.): (License restictions apply; see documentation)
MFIXReader, a library of routines that can read MFIX data files.: Source code is available.
MKL, Math Kernel Library, highly optimized and threaded routines for linear algebra, FFTs, vector math and random number generators.: (Pople, Salk, Warhol)
MODULE, a package which provides for the dynamic modification of a user environment.: (BigBen, Pople, Salk, Warhol)
MPI/ MPICH, Message Passing Interface, a communications substrate for scientific computing. MPICH, an implementation of MPI, was a joint-effort project between Argonne National Laboratories and Mississippi State University.: (BigBen, Opteron)
MPQC, Massively Parallel Quantum Chemistry program.: (BigBen)
MSA, a global multiple sequence alignment program that aligns several protein or nucleic acid sequences.: (Opteron)
NAMD, a parallel, object-oriented molecular dynamics code for the simulation of large biomolecular systems.: (Pople, Salk, BigBen, Warhol)
NBRF-PIR, National Biomedical Research Foundation Protein Identification Resource database. This database has been merged into the UniProt database. Please see the UniProt documentation.: (Opteron)
NCARGKS, a graphics library from the National Center for Atmospheric Research.: (BigBen)
NETCDF, an interface for array-oriented data access and a library that provides an implementation of the interface.: (Pople, BigBen)
NETLIB, an electronic repository, available through email and the WWW, of mathematical software, data, documents, address lists, and other useful items. In particular, take a look at toms and quadpack.
NQS2PBS, a utility to convert NQS jobs to PBS jobs.: (BigBen)
NRL-3D, a sequence-structure database derived from the 3D structure of proteins in the Brookhaven PDB. This database has been replaced by the PDB database.: (Opteron)
NWCHEM, uses quantum mechanical descriptions of electronic wavefunctions or density to compute the properties of molecular or periodic systems.: (Pople)
NWGAP, a global sequence alignment program.: (Opteron)
Open Inventor, an open source, object-oriented, 3-D toolkit for interactive graphics.: (Pople)
PAPI, an API for accessing hardware performance counters.: (Pople, BigBen)
PARAVIEW, open source program for the visualization of scientific, engineering, and analytical data.: (Pople)
PATCHX, a sequence structure database which is a subset of the merged MIPSX database. PATCHX has been replaced by the UniProt database.: (Opteron)
PETSC, a suite of routines for the solution of large scale scientific applications modeled by partial differential equations.: (BigBen, Pople, Warhol)
PFAM, a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.: (Opteron)
PGENESIS, developed at PSC to enable the well-known GENESIS neural simulator to run on a variety of parallel machines.: (BigBen)
PHAT, a tool for finding genes in eukaryotic organisms.: (Opteron)
PHYLIP, infers phylogenies and performs related tasks.: (Opteron)
PROFILE-SS, search database for multiple segments that align well with a profile.: (Opteron)
PROSITE, a Protein Database.: (Opteron)
PROTEIN DATA BANK (PDB), an archive of experimentally determined three-dimensional structures of biological macromolecules: (Opteron)
PY2DX, Python extensions for the OpenDX visualization package.: Source code is available.
RasMol, visualization of proteins, nucleic acids and small molecules, aimed at teaching, display, and generation of publication quality images.: (Opteron)
READSEQ, reformats nucleic acid or protein sequence files into a different format.: (Opteron)
REBASE, a restriction enzyme database.: (Opteron)
SAPS, evaluates by statistical criteria a wide variety of protein sequence properties.: (Opteron)
SCALAPACK , a linear algebra library for parallel machines.: (BigBen)
SEQSORT, sorts the output from sequence analysis programs.: (Opteron)
SPRNG, a scalable, parallel, pseudo-random number generator especially suited to large-scale parallel Monte-Carlo applications.: (BigBen)
Star-P, a tool designed to work with Matlab or Python and allow parallel execution of those codes on high-performance computing platforms.: (Pople)
StarSplatter, a tool to create images and animations from astrophysical particle simulation data.
SUPERLU, a subroutine library for solving sparse linear systems of equations AX = B.: (BigBen)
SWISS-PROT, the Swiss protein sequence database. This database has been merged into the UniProt database. Please see the UniProt documentation.: (Opteron)
TAU, Tuning and Analysis Utility.: (Pople, BigBen)
T-COFFEE, multiple sequence alignment.: (Opteron)
TOMSF, converts the output of one multiple sequence alignment program to the format used by another.: (Opteron)
TOTALVIEW, a source and machine-level debugger.: (Pople, BigBen)
TRANSTERM, a package to find rho-independent transcription terminators in bacterial genomes.: (Opteron)
UniProt, Universal Protein resource, a catalog of information on proteins. It comprises the information from the Swiss-Prot, TrEMBL and PIR libraries.: (Opteron)
UPC, Unified Parallel C.: (Pople, Salk, BigBen)