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)

AFS, the Andrew File System.
(Linux)

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, BigBen, Rachel, Jonas, Opteron)

ANSYS, finite element modeling package for solving a variety of mechanical problems.
(Rachel)

ATLAS, Automatically Tuned Linear Algebra Software.
(BigBen, Rachel)

ATV, a tool for the visualization of annotated phylogenetic trees.
(Opteron)

BLAS, routines for performing vector and matrix operations. See CXML.

BLASTZ, a multiple sequence alignment program for whole-genome human-mouse alignments.
(Opteron)

CAMBRIDGE, a crystallographic database. Academic users must make special arrangements for use. See the documentation for details.
(Opteron)

CHARMM, mechanics and dynamics of macromolecular systems. Academic and industrial users must make special arrangements for use. See the documentation for details.
(BigBen, Rachel, Jonas)

ComAlign, extracts qualitatively good sub alignments from a set of multiple alignments and combines them in a new, often improved alignment.
(Opteron)

CLUSTALW, a package of multiple alignment programs.
(Opteron)

CXML, the Compaq Extended Math Library, a set of mathematical routines optimized for Alpha systems.
(Rachel, Jonas)

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, Rachel)

FLUENT, a fluid dynamics solver which can model fluid flow and heat transfer in complex geometries.
(Pople, Rachel, Jonas)

FSHIFT, compares a protein query sequence with a translated DNA library sequence.
(Opteron)

GAMBIT, a preprocessor for Fluent.
(Rachel, Jonas)

GAMESS, an ab initio molecular quantum chemistry program.
(BigBen, Rachel)

GAUSSIAN, an ab initio quantum chemistry program. Academic and industrial users must make special arrangements for use. See the documentation for details.
(Pople, Salk, Rachel, Jonas)

GENBANK, Genetic Sequence Data Bank.
(Opteron)

GENEWISE, compares bio polymers, commonly DNA sequence and protein sequence.
(Opteron)

Goto BLAS, machine language, hand-coded, fast versions of the BLAS.
(Rachel)

GROMACS, molecular dymanics package.
(BigBen, Rachel)

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, Rachel)

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)

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)

MEME, a set of tools for discovering and using patterns in groups of related sequences.
(Opteron)

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)

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, Rachel, Jonas, 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, BigBen, Rachel, Jonas)

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)

NEDIT, a multi-purpose text editor with a GUI interface.
(Rachel, Jonas)

NETCDF, an interface for array-oriented data access and a library that provides an implementation of the interface.
(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, Rachel)

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.
(Rachel)

NWGAP, a global sequence alignment program.
(Opteron)

PAPI, an API for accessing hardware performance counters.
(BigBen)
PARAVIEW, open source program for the visualization of scientific, engineering, and analytical data.
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)

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, Rachel)

PHAT, a tool for finding genes in eukaryotic organisms.
(Opteron)

PHYLIP, infers phylogenies and performs related tasks.
(Opteron)

PMEMD, an improved Particle Mesh Ewald Molecular Dynamics simulation and minimization program.
(Rachel, Jonas)

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, Rachel)

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.
(BigBen)

THIRD DEGREE, a tool to show heap usage, and do leak profiling and memory-access error checking for C and C++ programs.
(Rachel, Jonas)

TOMSF, converts the output of one multiple sequence alignment program to the format used by another.
(Opteron)

TOTALVIEW, a source and machine-level debugger.
(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)