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

 

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

 

BayeScan

BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.

http://cmpg.unibe.ch/software/BayeScan/index.html

 

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/

 

BFAST

BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.

http://sourceforge.net/projects/bfast/

 

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

 

Breakdancer

Breakdancer is a package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.

http://breakdancer.sourceforge.net/

 

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

 

Clustal Omega

Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks.

http://www.clustal.org/omega/

 

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/

 

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

 

GenomeTools

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.

http://genometools.org/

 

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

 

InterProScan

InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.

http://www.ebi.ac.uk/interpro/interproscan.html

 

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/

 

MEME Suite

The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.

http://meme-suite.org/

 

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

 

miRDeep

miRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, …).

https://www.mdc-berlin.de/8551903/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep

 

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

 

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/

 

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

 

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/

 

pyRAD

The benefit of pyRAD over most alternative methods for analyzing RADseq-like data comes in its use of an alignment-clustering method (vsearch) that allows for the inclusion of indel variation which improves identification of homology across highly divergent samples. For this reason pyRAD is commonly employed for RADseq studies at deeper phylogenetic scales, however, it works equally well at shallow scales.

http://dereneaton.com/software/pyrad/

 

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/

 

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/

 

Scythe

Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads.

https://github.com/ucdavis-bioinformatics/scythe

 

ShortStack

ShortStack is a tool developed to process and analyze small RNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.

http://sites.psu.edu/axtell/software/shortstack/

 

Sickle

Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.

https://github.com/ucdavis-bioinformatics/sickle

 

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/

 

Stampy

Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome.

http://www.well.ox.ac.uk/project-stampy

 

Structure

The program Structure is a free software package for using multi-locus genotype data to investigate population structure.

http://pritchardlab.stanford.edu/structure.html

 

TASSEL

While TASSEL has changed considerably since its initial public release in 2001, its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes.

http://www.maizegenetics.net/#!tassel/c17q9

 

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

 

TransDecoder

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

https://transdecoder.github.io/

 

TRF

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

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

 

Trimmomatic

Trimmomatic is a flexible read trimming tool for Illumina NGS data.

http://www.usadellab.org/cms/index.php?page=trimmomatic

 

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/

 

VelvetOptimizer

VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.

http://bioinformatics.net.au/software.velvetoptimiser.shtml

 

Vienna RNA

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

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

 

VSEARCH

VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting.

https://github.com/torognes/vsearch

 

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/

 

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


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/

 

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/

 

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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.

 

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/

 

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/

 

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/

 

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/

 

Maxima

Maxima is a system for the manipulation of symbolic and numerical expressions.

http://maxima.sourceforge.net/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/

 

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

 

SageMath

SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.

http://www.sagemath.org/

 

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/

 

SPECFUN

SPECFUN is a FORTRAN90 library which evaluates certain special functions, by William Cody and Laura Stoltz.

https://people.sc.fsu.edu/~jburkardt/f_src/specfun/specfun.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


GMPT

GMT is Generic Mapping Tools

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

 

HDF

HDF is the Heirarchical Data Format library.

http://www.hdfgroup.org/

 

jModelTest

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

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

 

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/

 

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

 

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

 

CLISP

Gnu Common Lisp (clisp) is a feature-loaded implementation of a great language.

http://clisp.sourceforge.net/

 

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.

 

GNU Compilers

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

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

 

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/

 

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

 

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

 

NCAR Command Language

NCL is an intepretive language for scientific visualization.

http://www.ncl.ucar.edu

 

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/

 

ompP

ompP is a profiler for OpenMP parallelized software.

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

 

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/

 

TotalView

TotalView is a distributed memory parallel profiler and debugger.

http://www.roguewave.com/products-services/totalview

 

Valgrind

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

http://valgrind.org/

 

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/

 

ACES-III

ACES (Advanced Concept in Electronic Structure) is a quantum chemistry software package that implements coupled cluster methods for parallel computers.

http://www.qtp.ufl.edu/aces/index.shtml

 

CFOUR

CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules.

http://www.cfour.de/

 

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

 

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/

 

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/

 

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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VISUALIZATION


Circos

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

http://circos.ca

 

Grace

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

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

 

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/

 

Lynx

Lynx is a text based web browser.

http://lynx.browser.org/

 

Maestro

Maestro is a graphic interface for Jaguar.

http://www.schrodinger.com/

 

 

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/

 

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/

 

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


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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