*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)
**ABySS**, a de novo, parallel, paired-end sequence assembler designed for short reads.- (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)
**Blat**, (BLAST-Like Alignment Tool) identifies similarities between DNA sequences and protein sequences.- (Blacklight)
**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)
**DESMOND**, a molecular dynamics package.- (Blacklight)
**DRAWP3D**, a PSC developed 3D graphics library.- Source code is available.
**DReAMM**, PSC developed visualization package for MCell models.**FASTA Splitter**, a Perl script that divides FASTA files.- (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)
**GMP**, the Gnu Multiple Precision Arithmetic Library- (Blacklight)
**GNUPLOT**, an interactive 2-and 3-D function and data plotting program.- (Blacklight, Salk)
**GROMACS**, molecular dynamics package.- (Blacklight, Salk)
**HDF**(**H**ierarchical**D**ata**F**ormat), 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)
**Jellyfish**, a tool for fast, memory efficient counting of K-mers in DNA.- (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)
**MOLPRO**, a complete system of ab initio programs for molecular electronic structure calculations.- (Blacklight)
**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)
**Oases**, a de novo transcriptome assembler for very short reads.- (Blacklight)
**OCTAVE**, a high level language primarily intended for numerical computations that is mostly compatible with MATLAB.- (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)
**Pyrex**, a language specially designed for writing Python extension modules.- (Blacklight)
**PYTHON**, a powerful, object-oriented programming language.- (Blacklight)
**QT**, an application development framework- (Blacklight)
**Quake**, correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.- (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)
**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)
**SOAPsnp**, an accurate consensus sequence builder which calculates a quality score for each consensus base.- (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.**Tophat**, a fast splice junction mapper for RNA-Seq reads.- (Blacklight, BioU)
**TAU**, Tuning and Analysis Utility.- (Blacklight)
**TINKER**, a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.- (Blacklight)
**Trans-ABySS**, a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.- (Blacklight)
**TRINITY**, a package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data.- (Blacklight, BioU)
**UPC**, Unified Parallel C.- (Blacklight, Salk)
**VarScan**, detects variants in NGS data.- (Blacklight)
**Velvet**, a de novo genomic assembler specially designed for short read sequencing technologies- (Blacklight, BioU)