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/

 

antiSMASH

antiSMASH is a gene cluster detector.

http://antismash.secondarymetabolites.org/

 

BamTools

BamTools are a C++ API & command-line toolkit for working with BAM data.

https://github.com/pezmaster31/bamtools/wiki

 

Bcftools

Bcftools is a program for variant calling and manipulating VCFs and BCFs.

http://samtools.github.io/bcftools/

 

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/

 

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/

 

CD-HIT

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

http://weizhongli-lab.org/cd-hit/

 

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 alignment tool.

http://www.clustal.org/

 

ColinearScan

ColinearScan is a program for colinearity analysis of genomes.

http://colinear.cbi.pku.edu.cn/

 

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://cole-trapnell-lab.github.io/cufflinks/

 

Danpos

Danpos is a toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing. Version 2 is sometimes called DANPOS2.

https://sites.google.com/site/danposdoc/

 

EMu

EMu (Expectation-Maximisation inference of mutational signatures) is software for inferring the mutational signatures present in a number of cancer mutation sets.

http://www.sanger.ac.uk/resources/software/emu/

 

EvidentialGene

EvidentialGene is a genome informatics project for "Evidence Directed Gene Construction for Eukaryotes", for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University.

http://arthropods.eugenes.org/about/about-EvidentialGene/

 

ExaBayes

ExaBayes is a software package for Bayesian tree inference.

http://sco.h-its.org/exelixis/web/software/exabayes/index.html

 

eXpress

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

http://bio.math.berkeley.edu/eXpress/overview.html

 

Exonerate

Exonerate is a generic tool for pairwise sequence comparison.

https://www.ebi.ac.uk/~guy/exonerate/

 

FASTA

FASTA is an alignment program for bioinformatics.

http://faculty.virginia.edu/wrpearson/fasta/fasta_versions.html

 

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://code.google.com/p/garli/

 

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

 

GeneMarkS

Novel genomic sequences can be analyzed by the self-training program GeneMarkS for sequences longer than 50 kb.

http://exon.gatech.edu/GeneMark/

 

GeneTorrent

GeneTorrent is client software for downloading sequence data from CGHub's repository. The two main programs are gtdownload and cgquery.

https://cghub.ucsc.edu/software/downloads.html

 

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/

 

HMMER

Biosequence analysis using profile hidden Markov models.

http://hmmer.janelia.org

 

Iscan

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

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

 

jModelTest

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.

https://code.google.com/p/jmodeltest2/

 

MACS

MACS does Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa).

http://liulab.dfci.harvard.edu/MACS/

 

MAFFT

MAFFT is a multiple sequence alignment program.

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

 

MaSuRCA

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches.

http://www.genome.umd.edu/masurca.html

 

Mauve

Mauve - multiple genome alignment

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

 

MCScanX

MCScan is an algorithm to scan multiple genomes or subgenomes to identify putative homologous chromosomal regions, then align these regions using genes as anchors. MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity and extends the software by incorporating 15 utility programs for display and further analyses.

http://chibba.pgml.uga.edu/mcscan2/

 

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/

 

mothur

This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

http://www.mothur.org/wiki/Main_Page

 

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

 

Mugsy

Mugsy is a multiple whole genome aligner.

http://mugsy.sourceforge.net/

 

MUMmer

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

http://mummer.sourceforge.net/

 

MUSCLE

MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW.

http://drive5.com/muscle/

 

MuTect

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

http://www.broadinstitute.org/cancer/cga/mutect

 

myRAST

RAST (Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating complete or nearly complete bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree.

http://rast.nmpdr.org/

 

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

 

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://broadinstitute.github.io/picard/

 

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/

 

RepeatExplorer

RepeatExplorer includes utilities for Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data and tools for the detection of transposable element protein coding domains.

https://bitbucket.org/repeatexplorer/repeatexplorer

 

RepeatMasker

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

http://www.repeatmasker.org/

 

RevBayes

RevBayes is a statistical phylogenetics software project. It exploits the graphical models framework in developing flexible inference and simulation software for statistical problems in evolutionary biology, phylogenetics, and comparative genomics.

http://revbayes.github.io/intro.html

 

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/

 

SnpEff

SnpEff is a genetic variant annotation and effect prediction toolbox.

http://snpeff.sourceforge.net/

 

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

 

SPAdes

SPAdes is a genome assembly program.

http://bioinf.spbau.ru/en/spades

 

SRA

This is the Sequence Read Archive toolkit from NCBI. This is a three part tool; a download/upload client, .sra file conversion utilities, an encryption utility.

http://www.ncbi.nlm.nih.gov/sra

 

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.

https://ccb.jhu.edu/software/tophat/index.shtml

 

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

 

Trinotate

Trinotate is an annotation method suitable for computational assembled transcripts from RNAseq sequencing data.

https://trinotate.github.io/

 

VCFtools

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project.

http://vcftools.sourceforge.net/docs.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/

 


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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

 

Delft3D

Delft3D is a world leading 3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.

http://oss.deltares.nl/web/delft3d/home

 

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/

 

XBeach

XBeach is a two-dimensional model for wave propagation, long waves and mean flow, sediment transport and morphological changes of the nearshore area, beaches, dunes and backbarrier during storms.

http://oss.deltares.nl/web/xbeach/home

 

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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/

 

CCP4

CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.

http://www.ccp4.ac.uk/index.php

 

Coot

Coot, Crystallographic Object-Oriented Toolkit, is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.

http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

 

JuNoLo

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

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

 

Phenix

PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

https://www.phenix-online.org/

 

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/

 

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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/

 

ARPACK

ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

http://www.caam.rice.edu/software/ARPACK/

 

ATLAS

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

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

 

Bertini

Bertini is for the numerical solution of systems of polynomial equations.

http://bertini.nd.edu/

 

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://sourceforge.net/projects/blitz/

 

CSDP

CSDP is a C library of routines that implements a predictor corrector variant of the semidefinite programming algorithm of Helmberg, Rendl, Vanderbei, and Wolkowicz.

https://projects.coin-or.org/Csdp/

 

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.

https://www.tacc.utexas.edu/research-development/tacc-software/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/

 

Macaulay2

Macaulay2 is a software system devoted to supporting research in algebraic geometry and commutative algebra.

http://www.math.uiuc.edu/Macaulay2/

 

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/

 

OpenBLAS

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

http://www.openblas.net/

 

P3DFFT

Parallel Three-Dimensional Fast Fourier Transforms, dubbed P3DFFT, is a library for large-scale computer simulations on parallel platforms.

https://code.google.com/p/p3dfft/

 

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/

 

Singular

Singular is a computer algebra system for polynomial computations.

http://www.singular.uni-kl.de/

 

SLATEC

SLATEC Common Mathematical Library

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

 

UMFPACK

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

http://faculty.cse.tamu.edu/davis/suitesparse.html

 

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/

 

 

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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

 

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OTHER


ADH

ADH is a state-of-the-art ADaptive Hydraulics Modeling system developed by the Coastal and Hydraulics Laboratory, ERDC, USACE, and is capable of handling both saturated and unsaturated groundwater, overland flow, three-dimensional Navier-Stokes flow, and two- or three-dimensional shallow water problems.

http://chl.erdc.usace.army.mil/adh

 

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/

 

jModelTest

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.

https://code.google.com/p/jmodeltest2/

 

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/

 

LANDIS-II

LANDIS-II simulates forest succession, disturbance (including fire, wind, harvesting, insects), climate change, and seed dispersal across large (typically 10,000 - 20,000,000 ha) landscapes.

http://www.landis-ii.org/home

 

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.tetraresearch.com/locichem/about-locichem/

 

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/

 

SPA

The Soil-Plant-Atmosphere model (SPA, Williams et. al 1996) is a process-based model that simulates ecosystem photosynthesis and water balance at fine temporal and spatial scales (30 minute time-step, multiple canopy and soil layers).

https://www.wiki.ed.ac.uk/display/cesdwiki/SPA

 

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/

 

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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

 

CFITSIO

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

http://heasarc.gsfc.nasa.gov/fitsio/fitsio.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.hboehm.info/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/

 

Mono

Sponsored by Xamarin, Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.

http://www.mono-project.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.net/w/FrontPage

 

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.compressconsult.com/szip/

 

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/products-services/totalview

 

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/

 

XQilla

XQilla is an XQuery and XPath 2 library and command line utility written in C++, implemented on top of the Xerces-C library.

http://xqilla.sourceforge.net/HomePage

 

zlib
zlib is a general purpose data compression library.

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

 

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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://nbo6.chem.wisc.edu/

 

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.

https://orcaforum.cec.mpg.de/

 

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/

 

SIESTA

SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is a program for electronic structure molecular dynamics calculations with a localized basis set.

http://departments.icmab.es/leem/siesta/

 

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SEMIEMPIRICAL


MOPAC

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

http://openmopac.net/

 

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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/

 

ImageJ

ImageJ is an image processing and analysis program.

http://imagej.nih.gov/ij/

 

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/

 

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://www2.mmm.ucar.edu/wrf/OnLineTutorial/Graphics/RIP4/index.html/

 

Smokeview

Smokeview (SMV) is a visualization program used to display the output of FDS and CFAST simulations.

https://code.google.com/p/fds-smv/

 

surf

surf is a tool to visualize algebraic curves and algebraic surfaces.

http://sourceforge.net/projects/surf/

 

VisIT

VisIT - visualization software

https://wci.llnl.gov/simulation/computer-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/

 

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WEATHER MODELING


ARWpost

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

http://www2.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

 

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://esrl.noaa.gov/gsd/wrfportal/

 

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

 

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