Software installed on blacklight.psc.edu

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)

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)

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)

DMOL3, an ab initio quantum chemistry package.

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)

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)

Jellyfish, a tool for fast, memory efficient counting of K-mers in DNA.

(Blacklight)

LAMMPS, a classical molecular dynamics code.

(Blacklight)

LS-DYNA, a general purpose transient dynamic finite element program.

(Blacklight)

MATLAB, a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages.

(Blacklight)

MESA, an open source implementation of the OpenGL library.

(Blacklight)

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)

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)

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)

Pyrex, a language specially designed for writing Python extension modules.

(Blacklight)

PYTHON, a powerful, object-oriented programming language.

(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)

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)

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)

Tophat, a fast splice junction mapper for RNA-Seq reads.

(Blacklight, BioU)

TAU, Tuning and Analysis Utility.

(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)

Velvet, a de novo genomic assembler specially designed for short read sequencing technologies

(Blacklight, BioU)