Software and Tools

[BIOINFORMATICS] [ENGINEERING][MATERIALS SCIENCE][MATHEMATICS ][MOLECULAR DYNAMICS][OTHER][PROGRAMMING][QUANTUM CHEMISTRY][SEMIEMPIRICAL][VISUALIZATION ][WEATHER MODELING]


BIOINFORMATICS


ABySS

ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

http://www.bcgsc.ca/platform/bioinfo/software/abyss

 

ALLPATHS-LG

ALLPATHS-LG is a genome assembly tool developed at the Broad Institute.
It works on both small and large (mammalian size) genomes. To use it, you should first generate ~100 base Illumina reads from two libraries: one from ~180 bp fragments, and one from ~3000 bp fragments, both at about 45x coverage. Sequence from longer fragments will enable longer-range continuity.

http://www.broadinstitute.org/software/allpaths-lg/blog/

 

AMOS

AMOS is a collection of tools and class interfaces for the assembly of DNA reads.

http://sourceforge.net/projects/amos/

 

beagle-lib

beagle-lib is a library of GPU based functions for phylogenetic analysis.

http://code.google.com/p/beagle-lib/

 

BEAST

BEAST is a phylogenetic analysis program.

http://beast.bio.ed.ac.uk/Main_Page

 

BEDTools

BEDTools are a set of utilities for genomics analysis.

http://bedtools.readthedocs.org/en/latest/

 

BLAST+

BLAST+ searches one or more nucleic acid or protein databases for
BLAST+ sequences
similar to one or more query sequences of any type. BLAST+ can produce gapped alignments for the matches it finds.

http://rothlab.ucdavis.edu/genhelp/blast+.html

 

BLAT

BLAT (the BLAST-Like Alignment Tool) is a software program to identify similarities between DNA sequences and protein sequences.

http://genome.ucsc.edu/goldenPath/help/blatSpec.html

 

Bowtie

Bowtie is an ultrafast, memory-efficient short read aligner.

http://bowtie-bio.sourceforge.net/manual.shtml

 

Bowtie2

Bowtie2 is an ultrafast, memory-efficient short read aligner.

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

 

BWA

BWA (Burrows-Wheeler Aligner) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.

http://bio-bwa.sourceforge.net/

 

Celera Assembler

This software has multiple names; Celera Assembler, or wgs, which stands for Whole-Genome Shotgun Assembler

http://sourceforge.net/projects/wgs-assembler/

 

Centroid Fold

CentroidFold predicts an RNA secondary structure from an RNA sequence.

http://www.ncrna.org/software/centroidfold

 

ClustalW

ClustalW is a multiple sequence allignment tool.

http://www.clustal.org/

 

Cufflinks

Cufflinks is a reference-guided assembler for RNA-Seq experiments. It simultaneously assembles transcripts from reads and estimates their relative abundances, without using a reference annotation.

http://cufflinks.cbcb.umd.edu/manual.html

 

Edena

Edena is a de novo short reads assembler.

http://www.genomic.ch/edena.php

 

FastQC

FastQC is a Quality Control application for FastQ files.

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

 

FastX

The FastX-Toolkit includes FASTQ/A short-reads pre-processing tools.

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

 

GARLI

GARLI is a program that performs phylogenetic inference using the maximum-likelihood criterion.

https://www.nescent.org/wg_garli/Main_Page

 

GARM

GARM is (Genome Assembler, Reconcilation and Merging) a software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies.

http://garm-meta-assem.sourceforge.net/

 

GATK

The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers.

http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit

 

GMAP

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and
GSNAP: Genomic Short-read Nucleotide Alignment Program

http://research-pub.gene.com/gmap/

 

GSNAP

GSNAP: Genomic Short-read Nucleotide Alignment Program

http://research-pub.gene.com/gmap/

 

Iscan

Iscan (formerly twinscan and N-SCAN) is a suite of software for gene-structure prediction

http://mblab.wustl.edu/software.html

 

MAFFT

MAFFT is a multiple sequence alignment program.

http://mafft.cbrc.jp/alignment/software/

 

Mauve

Mauve - multiple genome alignment

module load mauve
http://asap.ahabs.wisc.edu/software/mauve/

 

MergeMap

MergeMap is a software tool that is capable of constructing accurate consensus genetic maps from a set of individual genetic maps.

http://alumni.cs.ucr.edu/~yonghui/mgmap.html

 

MetaVelvet

MetaVelvet: a short read assember for metagenomics

http://metavelvet.dna.bio.keio.ac.jp/

 

mpiBlast

mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST.

http://www.mpiblast.org/

 

MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

http://mrbayes.csit.fsu.edu/index.php

 

MUMmer

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.

http://mummer.sourceforge.net/

 

NCBI Toolbox

The NCBI Toolbox is a collection of bioinformatics programs.
This includes a number of frequently used tools such as blastall and formatdb.

http://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html

 

NextGenOptimator A5Pipeline

A5 is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform.

https://code.google.com/p/ngopt/

 

Oases

Oases is a De novo transcriptome assembler for very short reads.

http://www.ebi.ac.uk/~zerbino/oases/

 

PANDASEQ

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

https://github.com/neufeld/pandaseq

 

PHYLIP

PHYLIP is a free package of programs for inferring phylogenies.

http://evolution.genetics.washington.edu/phylip.html

 

PhyloBayes

PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other well suited for large multigene alignments, such as those used in phylogenomics.

http://www.atgc-montpellier.fr/phylobayes/

 

PhyloBayes-mpi

PhyloBayes-MPI is a Bayesian software for phylogenetic reconstruction using mixture models.

http://www.atgc-montpellier.fr/phylobayes/

 

Picard

Picard is a set of command line bioinformatics tools written in Java.

http://picard.sourceforge.net/command-line-overview.shtml

 

RANDFOLD

RANDFOLD is software that computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.

http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/

 

RAxML

RAxML is a tool for Maximum-likelihood based phylogenetic inference.

http://www.exelixis-lab.org/

 

Ray

Ray -- Parallel genome assemblies for parallel DNA sequencing

http://denovoassembler.sourceforge.net/index.html

 

Repbase

These are the repeat libraries for the program RepeatMasker.

http://www.girinst.org/repbase/

 

RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

http://www.repeatmasker.org/

 

RNA2MAP

This tool can be used to perform whole genome analysis of SOLiD™ RNA library reads.  It consists of three major procedures: filtering, matching against miRBase sequences (Sanger), and matching against a reference genome.

http://solidsoftwaretools.com/gf/project/rna2map/

 

SAMtools

SAMtools are for manipulating files in SAM (Sequence Alignment/Map) format, a generic format for storing large nucleotide sequence alignments.

http://samtools.sourceforge.net/

 

SHRiMP

SHRiMP is a software package for aligning genomic reads against a target genome.

http://compbio.cs.toronto.edu/shrimp/

 

SOAP3

SOAP3 is a GPU-based software for aligning short reads with a reference sequence.

http://soap.genomics.org.cn/soap3.html

 

SOAPdenovo

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes.

http://soap.genomics.org.cn/soapdenovo.html

 

SOAPdenovo-trans

SOAPdenovo-trans is a short-read assembly method similar to SOAPdenovo but without a "rank" parameter.

http://soap.genomics.org.cn/SOAPdenovo-Trans.html

 

SQUID

This is documentation on the SQUID Bioinformatics Library (not the SQUID web data caching server).

http://selab.janelia.org/software.html

 

Stacks

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.

http://creskolab.uoregon.edu/stacks/

 

TopHat

TopHat is a splice junction mapper for short RNA-Seq reads.  It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

http://tophat.cbcb.umd.edu/manual.html

 

TRF

Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.

http://tandem.bu.edu/trf/trf.html

 

Trinity

Trinity a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

http://TrinityRNASeq.sourceforge.net

 

Iscan

Iscan (formerly twinscan and N-SCAN) is a suite of software for gene-structure prediction

http://mblab.wustl.edu/software.html

 

Velvet

Sequence assembler for very short reads.

http://www.ebi.ac.uk/~zerbino/velvet/

 

Vienna RNA

Vienna RNA is a program for RNA secondary structure prediction and comparison.

http://www.tbi.univie.ac.at/~ivo/RNA/

 

WUBlast

The emphasis of this tool is to find regions of sequence similarity quickly, with minimum loss of sensitivity.

http://www.ebi.ac.uk/Tools/sss/wublast/

 


[Back to Top of Page]


ENGINEERING


CFD-ACE+ and CFD-FASTRAN

CFD-ACE+ and CFD-FASTRAN are commercial packages for computational fluid
dynamics.

https://www.esi-group.com/

 

CGNS

CGNS (CFD General Notation System)  provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.

http://cgns.sourceforge.net/index.html

 

Code_saturne

Code_Saturne is a public domain CFD code.

http://www.code-saturne.org

 

Hyperworks

Hyperworks is a GUI for Pre/Post processing for engineering applications.

http://www.altairhyperworks.com/?AspxAutoDetectCookieSupport=1

 

INS2D

The INS2D code solves the incompressible Navier-Stokes equations in two-dimensional generalized coordinates for both steady-state and time varying flow.

http://people.nas.nasa.gov/~rogers/ins2d/intro.html

 

INS3D

The INS3D code solves the incompressible Naiver-Stokes equations in three-dimensional generalized coordinates for both steady-state and time varying flow.

http://people.nas.nasa.gov/~rogers/ins3d/intro.html

 

OpenFOAM

OpenFOAM is primarily intended as a C++ library for building CFD solver applications and utilities.

http://www.openfoam.org/docs/

 

[Back to Top of Page]


MATERIALS SCIENCE


ATAT

ATAT stands for Alloy Theoretical Automated Toolkit It is a set of utilities that run on top of VASP

http://www.its.caltech.edu/~avdw/atat/

 

JuNoLo

JuNoLo is used as a post-processor for other codes, such as VASP.

http://iffwww.iff.kfa-juelich.de/iff_th1/JuNoLo/

 

XPLOR-NIH

XPLOR-NIH is a structure determination program which builds on the X-PLOR program, including additional tools developed at the NIH.

http://nmr.cit.nih.gov/xplor-nih/

 

[Back to Top of Page]


MATHEMATICS


ACML

AMD Core Math Library (ACML) is a library of mathematical functions, such as the BLAS (basic linear algebra subroutines) functions.  This library has been optimized for the best performance (fastest running codes) on the AMD Opteron CPUs.

 

ADMB

AD Model Builder, or ADMB is a powerful software package for the development of state-of-the-art nonlinear models

http://www.admb-project.org/

 

Armadillo

Armadillo is a C++ library of matrix algebra functions.

http://arma.sourceforge.net/

 

ATLAS

ATLAS math library - a BLAS and LAPACK implementation ATLAS stands for Automatically Tuned Linear Algebra Software

http://math-atlas.sourceforge.net/

 

Bessel

This is a locally complied installation of complex Bessel functions.

No web address

 

BLAS

BLAS is a set of Basic Linear Algebra Subroutines.  It is used to compile many scientific and mathematical software packages.

http://www.netlib.org/blas/

 

Blitz++

Blitz++ is a numerical mathematics library for C++.

http://www.oonumerics.org/blitz/whatis.html

 

deal.II

deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements. It uses state-of-the-art programming techniques to offer you a modern interface to the complex data structures and algorithms required.

http://www.dealii.org/

 

FFTW

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.

http://www.fftw.org/

 

gmp

The gmp library is the GNU Multiple Precision Arithmetic Library.  This is a set of routines for doing high accuracy calculations.

http://gmplib.org/

 

gotoBlas

gotoBlas is a math library created at the University of Texas.

http://www.tacc.utexas.edu/tacc-projects/gotoblas2

 

GSL

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.

http://www.gnu.org/software/gsl/

 

LAPACK

LAPACK is a Linear Algebra PACKage.  It is used to compile many scientific and mathematical software packages.

http://www.netlib.org/lapack/

 

Lapack++

LAPACK++ (Linear Algebra PACKage in C++) is a software library for
numerical linear algebra that solves systems of linear equations and eigenvalue problems on high performance computer architectures.

http://lapackpp.sourceforge.net/

 

METIS

METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.

http://glaros.dtc.umn.edu/gkhome/views/metis/index.html

 

MKL

MKL is a Math Kerenel Library sold by Intel.  It has standard math functions such as BLAS and LAPACK in an optimized, thread safe format.

http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/

 

Octave

Octave is a public domain clone of matlab.  It is about 95% compatible with Matlab.

http://www.octave.org/

 

ParMETIS

ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations.

http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview

 

PETSc

PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.

http://www.mcs.anl.gov/petsc/petsc-as/

 

R

R is a free software environment for statistical computing and graphics.

http://www.r-project.org/

 

ROOT

ROOT is a data analysis framework.

http://root.cern.ch/drupal/content/downloading-root

 

SCOTCH

SCOTCH is a software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.

http://www.labri.fr/perso/pelegrin/scotch/

 

SLATEC

SLATEC Common Mathematical Library

http://www.netlib.org/slatec/

 

UMFPACK

UMFPACK is a set of routines for solving unsymmetric sparse linear systems.

http://www.cise.ufl.edu/research/sparse/umfpack/

 

Voro++

Voro++ is a open source software library for the computation of the
Voronoi diagram, a widely-used tessellation that has applications in many scientific fields.

http://math.lbl.gov/voro++/about.html

 

Wind-US

Wind-US is a computational platform which may be used to numerically solve various sets of equations governing physical phenomena.

http://www.grc.nasa.gov/WWW/winddocs/

 

 

[Back to Top of Page]


MOLECULAR DYNAMICS


Amber

Amber (Assisted Model Building with Energy Refinement) "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

http://ambermd.org/

 

Autodock

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

http://autodock.scripps.edu/faqs-help

 

GROMACS

GROMACS is a versatile package to perform molecular dynamics, i.e.
simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

http://www.gromacs.org

 

LAMMPS

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

http://lammps.sandia.gov/

 

NAMD

NAMD is a molecular dynamics program.

http://www.ks.uiuc.edu/Research/namd/

 

OpenKIM

OpenKIM is a library of functions that implements and api for KIM (Knowledgebase of Interatomic Models), which is used by some molecular simulation codes.

http://www.openkim.org/

 

OpenMM

OpenMM is a library of molecular mechanics functions for GPU chips.
It is used to install the GPU capable versions of GROMACS and AMBER.

https://simtk.org/home/openmm

 

[Back to Top of Page]


OTHER


AFNI

AFNI (which might be an acronym for Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data.

http://afni.nimh.nih.gov/afni

 

Babel

Open Babel is a free, open-source version of the Babel chemistry file translation program. OpenBabel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.

http://openbabel.sf.net/

 

GMPT

GMT is Generic Mapping Tools

from http://gmt.soest.hawaii.edu/

 

HDF

HDF is the Heirarchical Data Format library.

http://www.hdfgroup.org/

 

HepMC

The HepMC package is an object oriented event record written in C++ for High Energy Physics Monte Carlo Generators.

http://lcgapp.cern.ch/project/simu/HepMC/

 

Herwig++

Herwig++ is an event generator written in C++.

https://herwig.hepforge.org/

 

Kintecus

Kintecus is a powerful Industrial Strength/Research Grade chemical modeling software for simulation of combustion, nuclear, biological, enzyme, atmospheric and many other chemical kinetic and equilibrium processes.

http://www.kintecus.com/

 

Linpack

The Linpack benchmark is a matrix algebra benchmark that has been around quite a few years.

http://www.netlib.org/utk/people/JackDongarra/faq-linpack.html

 

Loci-Chem

Loci-Chem is a complex multiphysics simulation package.

http://www.cse.msstate.edu/~luke/chem/

 

m5sim

M5 is a processor and system simulator developed at the University of Michigan.

http://m5sim.org/wiki/index.php/Documentation

 

QIIME

QIIME (canonically pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities.

http://qiime.org/

 

Swami

Swami is a utility under development at the Alabama Supercomputer Center.  It is designed to give an estimate of how much CPU time and memory a computational chemistry calculation will take.

no web site

 

ThePEG

Toolkit for High Energy Physics Event Generation

http://home.thep.lu.se/~leif/ThePEG/

 

tmux

tmux is a terminal multiplexer: it enables a number of terminals (or windows), each running a separate program, to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached.

http://tmux.sourceforge.net/

 

[Back to Top of Page]


PROGRAMMING


Boost

Boost is a library of additional functionality for C++.
A number of the items in Boost are functionality that is under consideration for inclusion in future verisons of the C++ standard.

http://www.boost.org/

 

byacc

Berkley yacc is a yacc program that may be needed to install selected software programs.  In order to put the byacc paths in your account, use the following

http://invisible-island.net/byacc/byacc.html

 

cmake

cmake is a cross platform make utility.

http://www.cmake.org/

 

CUDA

CUDA is a GPU programming language based on C.

http://developer.nvidia.com/nvidia-gpu-computing-documentation

 

CxxTest

CxxTest is a C++ unit test harness that was highly recommended by several reviewers.

http://cxxtest.tigris.org/

 

Delphes

Delphes is a C++ framework, performing a fast multipurpose detector response simulation.

https://cp3.irmp.ucl.ac.be/projects/delphes

 

Eclipse_ptp

Eclipse is a graphical source code editing program.

http://eclipse.org/ptp/doc.php

 

f2c

f2c is a program to convert fortran source code to C source code.

No web address.

 

g2clib

g2clib is a library of functions for encoding and decoding data in the GRIB2 format.

http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/

 

GNU Compilers

C, C++, and Fortran compilers from the GNU project.

http://www.g95.org/docs.html

 

GASNet

GASNet is a language-independent, low-level networking layer that provides network-independent, high-performance communication primitives tailored for implementing parallel global address space SPMD languages such as UPC, Titanium, and Co-Array Fortran.

http://gasnet.cs.berkeley.edu/

 

GC

GC is the Hans Boehm garbage collector library for C and C++

http://www.hpl.hp.com/personal/Hans_Boehm/gc/

 

GDAL

GDAL is a translator library for raster geospatial data formats.

http://www.gdal.org/

 

gdb

gdb is the GNU project debugger

http://www.sourceware.org/gdb/

 

Git

Git is a version control system for managing source code trees.

http://git-scm.com/doc

 

GLEW

The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library.

http://glew.sourceforge.net/

 

gmake

GNU Make is a software compilation program.

http://www.gnu.org/software/make/

 

HPCToolkit

HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation's largest supercomputers.  HPCToolkit provides accurate measurements of a program's work, resource consumption, and inefficiency, correlates these

http://hpctoolkit.org/documentation.html

 

Intel compilers

Intel compilers for C, C++ and Fortran.

http://software.intel.com/en-us/intel-compilers

 

JasPer

The JasPer libraries are jpeg-2000 libraries.

http://www.ece.uvic.ca/~mdadams/jasper/

 

Java

Java is a cross-platform graphical programming language.

https://www.java.com/en/

 

libcurl

libcurl is library for internet transfer functions.

http://curl.haxx.se/libcurl/

 

libgtextutils

libgtextutils are a prerequisite to installing fastx

http://hannonlab.cshl.edu/fastx_toolkit/download.html

 

libpng

libpng is a library of functions for reading and writing .png files (portable network graphics).

http://www.libpng.org/pub/png/libpng.html

 

libxml2

Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License.

http://xmlsoft.org/

 

libyaml

LibYAML is a YAML 1.1 parser and emitter written in C.

http://pyyaml.org/wiki/LibYAML

 

LISP

GCL is the official Common Lisp for the GNU project.

http://www.gnu.org/software/gcl/

 

Lua

Lua is a powerful, fast, lightweight, embeddable scripting language.

http://www.lua.org/

 

Mercurial

Mercurial is a version control system for managing source code trees.

http://mercurial.selenic.com/

 

MPE2

MPE is a software package for MPI programmers that provides a number of useful tools for profiling and visualizing MPI programs.

https://www.olcf.ornl.gov/kb_articles/software-mpe2/

 

MPI

MPI stands for Message Passing Interface.  It is a library of functions for writing software that can distribute work across multiple servers on a network.

http://www.open-mpi.org/

 

MPInside

MPInside is a SGI provided profiler for MPI parallelized software.

http://techpubs.sgi.com/library/manuals/5000/007-5780-001/pdf/007-5780-001.pdf

 

MuParser

MuParser is an equation parsing library in C++.

http://muparser.beltoforion.de/

 

NCAR Command Language

NCL is an intepretive language for scientific visualization.

http://www.ncl.ucar.edu

 

NEXUS Class Library

The NEXUS Class Library (NCL) is an integrated collection of C++ classes designed to allow the user to quickly write a program that reads NEXUS-formatted data files. It also allows easy extension of the NEXUS format to include new blocks of your own design.

http://hydrodictyon.eeb.uconn.edu/ncl/

 

NetCDF

NetCDF (network Common Data Form) is a set of software libaries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

http://www.unidata.ucar.edu/software/netcdf/

 

Objective Caml

Objective Caml is an object-oriented extension of the Caml language.
It has both a native compiler and a bytecode compiler.

http://caml.inria.fr/pub/docs/manual-ocaml/index.html

 

ompP

ompP is a profiler for OpenMP parallelized software.

http://www.ompp-tool.com/

 

OpenBUGS

OpenBUGS is a software package for performing Bayesian inference Using Gibbs Sampling.

http://www.openbugs.info/w/

 

OpenCV

OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.

http://opencv.org/

 

PAPI

PAPI's intended audience includes application developers, performance tool writers, and curious students of performance who wish to access performance data to tune and model application performance. You should have some level of familiarity with C and Fortran, and have a basic knowledge of computer architecture and programming.

http://icl.cs.utk.edu/projects/papi/wiki/Main_Page

 

perfcatcher

perfcatcher is an SGI utility for profiling software written with MPT or SHMEM.

http://techpubs.sgi.com/library/tpl/cgi-bin/getdoc.cgi?coll=linux&db=man&fname=/usr/share/catman/man1/perfcatch.1.html

 

Perl

Perl 5 is a highly capable, feature-rich programming language with over 26 years of development.

http://www.perl.org/

 

Portland Group Compilers

The Portland group compilers are compilers for C, C++, and Fortran.

http://www.pgroup.com

 

Python

Python is a programming language that lets you work more quickly and integrate your systems more effectively.

http://www.python.org/doc/

 

Qt

Qt is a set of graphical display routines that run on multiple operating systems.

https://qt-project.org/

 

SIP

SIP is a software tool for generating Python bindings for software C and C++ libraries, and a Python extension module used at runtime by those generated bindings.

http://www.riverbankcomputing.co.uk/software/sip/download

 

sparsehash

sparsehash (also known as google-sparsehash) is an extremely memory-efficient hash_map implementation. 2 bits/entry overhead!
The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed.

http://code.google.com/p/google-sparsehash/

 

SQlite

SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine. SQLite is the most widely deployed SQL database engine in the world. The source code for SQLite is in the public domain.

http://www.sqlite.org/

 

Subversion

Subversion is an open source version control system.

http://subversion.apache.org/

 

SWIG

SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.

http://www.swig.org/

 

szip

Szip is a freeware portable general purpose lossless compression program.

http://www.hdfgroup.org/ftp/lib-external/szip/2.0/

 

TAMU ANOVA

TAMU ANOVA stands for Texas A&M University Analysis of Variation Algorithm.
This is a math library.

http://search.cpan.org/~vdanjean/Math-TamuAnova-1.0.2/lib/Math/TamuAnova.pm

 

TotalView

TotalView is a distributed memory parallel profiler and debugger.

http://www.roguewave.com/support/product-documentation.asp

 

Trilinos

The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.

http://trilinos.sandia.gov

 

Unified Parallel C

Unified Parallel C (UPC to it's friends) is an extension of the C programming language designed for high performance computing on large-scale parallel machines.

http://upc.gwu.edu/

 

Valgrind

Valgrind includes a collection of dynamic program analysis tools to assist in programming errors and application profiling.

http://valgrind.org/

 

Xerces

Xerces is a C++ library of XML functions.

http://xerces.apache.org/xerces-c/

 

zlib
zlib is a general purpose data compression library.

http://www.gzip.org/zlib/zlib_faq.html

 

[Back to Top of Page]


QUANTUM CHEMISTRY


ABINIT

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

http://www.abinit.org/

 

CPMD

The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.

http://www.cpmd.org/cpmd_faq.html

 

GAMESS

The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.

http://www.msg.ameslab.gov/gamess/

 

Gaussian

Gaussian is a popular quantum chemistry software packages.

http://www.gaussian.com

 

Gaussrate

Gaussrate provides an interface between Polyrate and Gaussian.

http://comp.chem.umn.edu/gaussrate/

 

Gaussview

Gaussview is a graphic interface for the Gaussian software.

http://www.gaussian.com/g_prod/gv5.htm

 

Jaguar

Rapid ab initio electronic structure package.

http://www.schrodinger.com/productpage/14/7/

 

NBO

There are NBO functions that come with the Gaussian program.
However, there is also an add on package to Gaussian that installs extended NBO functionality.  Both are available at the Alabama Supercomputer Center.

http://www.chem.wisc.edu/~nbo5/nbo59.ht

 

NWChem

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

http://www.nwchem-sw.org/index.php/Main_Page

 

OpenMX

OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions.

http://www.openmx-square.org/

 

ORCA

ORCA is a flexible, reasonably efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to correlated ab initio methods. It can also treat environmental and relativistic effects.

http://www.thch.uni-bonn.de/tc/orca/

 

Polyrate

Polyrate is a Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics.

http://comp.chem.umn.edu/polyrate/

 

PSI4

PSI4 is an ab initio quantum chemistry program.

http://www.psicode.org/

 

Quantum Espresso

Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

http://www.quantum-espresso.org/

 

[Back to Top of Page]


SEMIEMPIRICAL


MOPAC

MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation.

http://openmopac.net/manual/index.htm

 

[Back to Top of Page]


VISUALIZATION


Blender

Blender is a free open source 3D content creation suite.

http://www.blender.org/

 

Circos

Circos is a software package for visualization, which is popular for displaying biological data.

http://circos.ca

 

ECCE

ECCE is a graphic interface for building molecular geometries, submitting jobs, and viewing results.  It can import and export many file formats.

http://ecce.emsl.pnl.gov/

 

FFmpeg

FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. It includes libavcodec - the leading audio/video codec library.

http://www.ffmpeg.org/

 

FigureGen

FigureGen is a program for generating graphics files from ADCIRC data.

http://www.caseydietrich.com/2012/06/05/figuregen-v-49/

 

Grace

Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif.

http://plasma-gate.weizmann.ac.il/Grace/

 

GrADS

The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data.

http://www.iges.org/grads/gadoc/index.html

 

Graphviz

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks.

http://www.graphviz.org/

 

Jmol

Jmol is a viewer for chemical structure data.

http://jmol.sourceforge.net/

 

LuxRender

LuxRender is a ray tracing render engine.

http://www.luxrender.net/wiki/Main_Page

 

Lynx

Lynx is a text based web browser.

http://lynx.browser.org/

 

Maestro

Maestro is a graphic interface for Jaguar.

http://www.schrodinger.com/

 

MGLTools

MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures.

http://mgltools.scripps.edu/

 

NCAR Graphics

NCAR Graphics is a Fortran and C based software package for scientific visualization.

http://ngwww.ucar.edu/ng4.4/documentation.html

 

Paraview

Paraview is an open-source, data analysis and visualization application.

http://www.paraview.org/Wiki/ParaView

 

Ploticus

Ploticus is a free GPL software utility that can produce various types of plots and graphs.

http://ploticus.sourceforge.net/doc/welcome.html

 

PyMOL

PyMOL is an OpenGL based molecular visualization system

http://www.pymol.org/

 

RIP4

RIP (which stands for Read/Interpolate/Plot) is a Fortran program that invokes NCAR Graphics routines for the purpose of visualizing output from gridded meteorological data sets, primarily from mesoscale numerical models.

http://www.mmm.ucar.edu/wrf/users/graphics/RIP4/RIP4.htm

 

Treeviz

Treeviz is a graphical program for visualization of large tree structures.

http://www.randelshofer.ch/treeviz/

 

VisIT

VisIT - visualization software

https://wci.llnl.gov/codes/visit/

 

VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

http://www.ks.uiuc.edu/Research/vmd/

 

XCrySDen

XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.

http://www.xcrysden.org/XCrySDen.htm

 

[Back to Top of Page]


WEATHER MODELING


ARWpost

ARWpost is a Fortran program that reads WRF-ARW input and output files, then generates GrADS output files.

http://www.mmm.ucar.edu/wrf/users/graphics/ARWpost/ARWpost.htm

 

BUFRLIB

NCEP BUFRLIB is a function library used by some weather modeling programs.

http://www.nco.ncep.noaa.gov/sib/decoders/BUFRLIB/

 

MET

MET is a data manipulation and analysis utility for weather modeling data.

http://www.dtcenter.org/met/users/metoverview/index.php

 

MM5

MM5 is a weather modeling code.

http://www.mmm.ucar.edu/mm5/

 

UPP

UPP is a post processor for use with WRF.

http://www.dtcenter.org/wrf-nmm/users/docs/user_guide/V3/users_guide_nmm_chap7.pdf

 

WPS

WPS is a preprocessing program for the WRF weather modeling program.

http://www.mmm.ucar.edu/wrf/users/wpsv2/wps.html

 

WRF

The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both atmospheric research and operational forecasting needs.

http://www.wrf-model.org/index.php

 

[Back to Top of Page]