Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing,
communications and data analytics.

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.
(Blacklight)
ADINA, a general linear and nonlinear finite element analysis system.
(Blacklight)
ALLPATHS-LG, a whole-genome shotgun assembler.
(Blacklight)
AMBER, uses classical mechanics to study large molecules.
(Blacklight, Salk)
ANSYS, a general purpose finite element modeling package for solving a wide variety of mechanical problems.
(Blacklight)
Bedops, a suite of tools to address common questions raised in genomics studies.
(Blacklight)
BEDTools, a collection of utilities for comparing, summarizing, and intersecting genomic features in the UCSC Genome Browser BED format.
(Blacklight, Biou)
BLAS, routines for performing vector and matrix operations.
(Blacklight, Salk)
Bowtie, an ultrafast, memory-efficient short read aligner.
(Blacklight, BioU)
BWA, a fast light-weighted tool that aligns relatively short sequences to a sequence database.
(Blacklight, BioU)
Celera Assembler, a de novo whole-genome shotgun (WGS) DNA sequence assembler.)
(Blacklight, BioU)
CHARMM, mechanics and dynamics of macromolecular systems. Academic and industrial users must make special arrangements for use. See the documentation for details.
(Blacklight, Salk)
CPMD, a parallelized, plane wave/pseudo-potential DFT package, designed for ab-inito molecular mechanics.
(Blacklight)
Cushaw, an open-source, parallelized, sensitive and accurate short-read aligner
(Blacklight)
DESMOND, a molecular dynamics package.
(Blacklight)
DRAWP3D, a PSC developed 3D graphics library.
Source code is available.
FASTA Splitter, a Perl script that divides FASTA files.
(Blacklight)
Fastqc, a quality control tool for high throughput sequence data
(Blacklight)
Fastx, a collection of command-line tools for Short-Reads FASTA/FASTQ files preprocessing
(Blacklight)
FFTW, a C subroutine library for computing Discrete Fourier Transforms.
(Blacklight, Salk)
FLUENT, a fluid dynamics solver which can model fluid flow and heat transfer in complex geometries.
(Blacklight)
GAMESS, an ab initio molecular quantum chemistry program.
(Blacklight)
GAUSSIAN, an ab initio quantum chemistry program. Academic and industrial users must make special arrangements for use. See the documentation for details.
(Blacklight, Salk)
GlimmerHMM, a Eukaryotic Gene-Finding System based on a Generalized Hidden Markov Model (GHMM)
(Blacklight, Biou)
Glimmer3, a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea and viruses
(Blacklight, Biou)
GNUPLOT, an interactive 2-and 3-D function and data plotting program.
(Blacklight, Salk)
GROMACS, molecular dynamics package.
(Blacklight, 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.
(Blacklight)
IPM, performance profiling tool for parallel MPI applications.
(Blacklight)
LAMMPS, a classical molecular dynamics code.
(Blacklight)
LAPACK, a linear algebra library.
(Blacklight)
LS-DYNA, a general purpose transient dynamic finite element program.
(Blacklight)
LSMS, uses the locally self-consistent multiple scattering method to calculate the electronic structure of large systems within the local density approximation.
(Contact PSC for more information)
MATLAB, a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages.
(Blacklight)
MCELL, (Monte Carlo Cell), simulates the movements and reaction of molecules within and between cells.
(Salk)
MESA, an open source implementation of the OpenGL library.
(Blacklight)
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)
MKL, Math Kernel Library, highly optimized and threaded routines for linear algebra, FFTs, vector math and random number generators.
(Blacklight, Salk)
Module, a package which provides for the dynamic modification of a user environment.
(Blacklight, Salk)
MPFR, a C library for multiple-precision floating-point computations with correct rounding.
(Blacklight)
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.
(Blacklight, Salk)
NAMD, a parallel, object-oriented molecular dynamics code for the simulation of large biomolecular systems.
(Blacklight, Salk)
NETCDF, an interface for array-oriented data access and a library that provides an implementation of the interface.
(Blacklight)
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.
NWCHEM, uses quantum mechanical descriptions of electronic wavefunctions or density to compute the properties of molecular or periodic systems.
(Blacklight)
OpenFOAM, an open source finite volume CFD package.
(Blacklight)
PAPI, an API for accessing hardware performance counters.
(Blacklight)
PARAVIEW, open source program for the visualization of scientific, engineering, and analytical data.
(Blacklight)
PETSC, a suite of routines for the solution of large scale scientific applications modeled by partial differential equations.
(Blacklight)
Picard, a set of Java-based command-line utilities that manipulate SAM (Sequence Alignment/Map)files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files.
(Blacklight, BioU)
Prodigal, an open source lightweight microbial genefinding program.
(Blacklight, BioU)
PSI4, an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties
(Blacklight)
Python, a powerful, object-oriented programming language.
(Blacklight)
Quantum Espresso, an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale.
(Blacklight)
R, a language and environment for statistical computing and graphs.
(Blacklight)
SAMtools, various utilities for manipulating alignments in the SAM (Sequence Alignment/Map) format.
(Blacklight, BioU)
SCALAPACK, a linear algebra library for parallel machines.
(Blacklight)
Sickle, a windowed adaptive trimmng tool for FASTQ files using quality
(Blacklight)
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and associated software to do electronic structure calculations and ab initio molecular dynamics simulations.
(Blacklight)
SNAP, a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes  
(Blacklight, Biou)
SOAPdenovo, a short read de novo assembly tool which assembles short oligonucleotide into contigs and scaffolds.
(Blacklight)
SomaticSniper, a program to identify single nucleotide positions that are different between tumor and normal cells  
(Blacklight, Biou)
StarSplatter, a tool to create images and animations from astrophysical particle simulation data.
SVDetect, a tool to detect genomic structural variations from paired-end and mate-pair sequencing
    (Blacklight)
TAU, Tuning and Analysis Utility.
(Blacklight)
Tabix, a generic indexer for TAB-delimited genome position data
(Blacklight)
TINKER, a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
(Blacklight)
Trinity, a package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data.
(Blacklight, BioU)
Trinotate, an annotation method suitable for computationally assembled transcripts from RNAseq sequencing data
(Blacklight)
UPC, Unified Parallel C.
(Blacklight, Salk)
VarScan, detects variants in NGS data.
(Blacklight)
VCFtools, a tool which provides easily accessible methods for working with complex genetic variation data in the form of VCF files
(Blacklight)
Velvet, a de novo genomic assembler specially designed for short read sequencing technologies
(Blacklight, BioU)