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User:YULdigitalpreservation/Scientific software list

Scientific SoftwareEdit

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label description image logo image license software version identifier depends on software developer file extension platform programming language operating system media type user manual link bug tracking system official website readable file format writable file format
.NET Bio software
1000Minds vomgjOnline decision-making and conjoint analysis software company https://www.1000minds.com
2D gel analysis software software
3D Virtual Creature Evolution evolution simulation program https://3dvce.fandom.com/wiki/Main_Page
A.nnotate web service for storing and annotating documents http://a.nnotate.com/ Portable Document Format
Abalone molecular dynamics and molecular graphics computer program proprietary license http://www.biomolecular-modeling.com/Abalone/Manual.html http://www.biomolecular-modeling.com/Abalone/ HyperChem Input File
SYBYL line notation
Protein Data Bank
XYZ file format
MLM
HyperChem Input File
Protein Data Bank
XYZ file format
MLM
Accelerator Physics Codes software
Affymetrix GeneChip Operating Software software system for managing Affymetrix microarray data Affymetrix https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html
Agfa impax 6 software Agfa-Gevaert
AIMAll quantum chemistry software package proprietary license Microsoft Windows
macOS
Linux
http://aim.tkgristmill.com/index.html Portable Network Graphics
Tagged Image File Format
JPEG File Interchange Format
Windows Bitmap
Portable Document Format
ALEGRA software Sandia National Laboratories http://www.cs.sandia.gov/ALEGRA/Alegra_Home.html
ALGOR finite element analysis software Linux
AlleleID desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification Microsoft Windows
macOS
http://www.premierbiosoft.com/bacterial-identification/index.html FASTA format
GenBank file format
Amira software platform for 3D and 4D data visualization Zuse Institute Berlin
Thermo Fisher Scientific
Windows XP https://www.fei.com/software/amira-user-guide/ https://www.fei.com/software/amira-avizo/
http://www.amira.com
Windows Bitmap
Drawing Interchange Format
HyperText Markup Language
Digital Imaging and Communications in Medicine
Protein Data Bank
Virtual Reality Modeling Language
Polygon File Format
AmiraMesh ASCII file format
AmiraMesh 3D ASCII 2.0 file format
AmiraMesh 3D Binary 2.0 file format
AmiraMesh 3D Binary Little Endian 2.0 file format
AmiraMesh Binary Little Endian 2.1 file format
Encapsulated PostScript
Windows Bitmap
Drawing Interchange Format
Wavefront .obj file
Virtual Reality Modeling Language
Polygon File Format
AmiraMesh ASCII file format
AmiraMesh 3D ASCII 2.0 file format
AmiraMesh 3D Binary 2.0 file format
AmiraMesh 3D Binary Little Endian 2.0 file format
AmiraMesh Binary Little Endian 2.1 file format
AnimatLab neuromechanical simulation software C++ http://animatlab.com
AnyLogic software for cross-platform and Java Virtual Machine, from 2000 7.1.2
7.3.2
Java Virtual Machine Java cross-platform http://www.anylogic.com
Aphelion image processing and analysis software suite 4.4.0 C# Microsoft Windows http://www.adcis.net/en/Download/Help-Files.html http://www.adcis.net/en/Products
http://www.adcis.net/en/Products/Aphelion-Imaging-Software-Suite.html
Application Mapper multiple sequence alignment software program http://bio.math.berkeley.edu/amap/download/ FASTA format FASTA format
Clustal file format
Aqion hydrochemistry software tool freeware 6.1.0 C++ Microsoft Windows http://www.aqion.de/site/98 http://www.aqion.de
Archaeopteryx software for viewing, editing, and analyzing phylogenetic trees 0.9917 Java Microsoft Windows
Linux
macOS
https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/documentation https://sites.google.com/site/cmzmasek/home/software/archaeopteryx
https://sites.google.com/site/cmzmasek/home/software/forester
PhyloXML
Nexus file
Nexus file
PhyloXML
Archim freeware program for making graphs in two or three dimensions freeware http://www.stochastic-lab.com:80/archim.html
Arlequin population genetics software 3.5.2.2 Swiss Institute of Bioinformatics http://popgen.unibe.ch/software/arlequin35/man/Arlequin35.pdf http://cmpg.unibe.ch/software/arlequin3/
ArrayTrack multi-purpose bioinformatics software tool 1.0.0
3.4.0
Food and Drug Administration https://www.fda.gov/downloads/ScienceResearch/BioinformaticsTools/Arraytrack/UCM250045.pdf http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm
Artificial intuition software
ASReml software for Microsoft Windows and Linux Microsoft Windows
Linux
https://www.vsni.co.uk/software/asreml/
ASTOS software for Microsoft Windows and Linux, from 1989 Microsoft Windows
Linux
http://www.astos.de
http://www.astos.de/products/astos
Atlas.ti computer program proprietary license Microsoft Windows
macOS
Android
http://atlasti.com/manuals-docs/ http://www.atlasti.com/
Atomistix ToolKit software for atomic-scale modeling and simulation of nanosystems Atomistix http://docs.quantumwise.com/manuals/manual.html http://www.quantumwise.com/ NetCDF NetCDF
Atomistix Virtual NanoLab software
Auto-Latex Equations Google Docs add-on for latex equations https://sites.google.com/site/autolatexequations/home
Autochem automatic code generator and documentor for atmospheric chemistry modeling David Lary Fortran 90 http://www.science-softcon.de/autochem/index.html
Autodesk Ecotect Analysis environmental analysis tool that allows designers to simulate building performance Autodesk
Automated Anatomical Labeling software package and digital atlas of the human brain MATLAB
SPM
http://www.cyceron.fr/index.php/en/plateforme-en/freeware
Automated Data Inquiry for Oil Spills software model for oil weathering National Oceanic and Atmospheric Administration Microsoft Windows
macOS
http://response.restoration.noaa.gov/oil-and-chemical-spills/oil-spills/response-tools/downloading-installing-and-running-adios.html
Avizo software for scientific and industrial data visualization and analysis http://www.vsg3d.com
aXe Spectral Extraction software European Space Agency http://axe-info.stsci.edu/
BAli-Phy software http://www.bali-phy.org/
http://www.bali-phy.org
Baudline software FreeBSD
Linux
Solaris
macOS
http://www.baudline.com
Beacon designer software for the design of primers and probes for real time PCR assays Premier Biosoft http://www.premierbiosoft.com/molecular_beacons/index.html GenBank file format
FASTA format
SNP file format
GenBank file format
FASTA format
SNP file format
tab-separated values
Bellerophon software for detecting chimeric sequences in multiple sequence datasets http://comp-bio.anu.edu.au/bellerophon/bellerophon.pl Sequence Alignment/Map
Berkeley Madonna mathematical modelling software package George Oster C
Java
Microsoft Windows
macOS
https://mcb.berkeley.edu/courses/mcb137/exercises/madonnamanual.pdf http://www.berkeleymadonna.com plaintext plaintext
comma-separated values
Bilbao Crystallographic Server website offering online crystallographic database and programs http://www.cryst.ehu.es
Bing Maps Platform geospatial mapping platform by Microsoft Microsoft Microsoft Windows http://www.microsoft.com/maps/
BioBIKE cloud-based bioinformatics platform MIT license Common Lisp http://www.biobike.org
http://biobike.csbc.vcu.edu/
Bioconductor software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology Artistic License http://www.bioconductor.org
http://www.bioconductor.org/
BioExtract bioinformatics software http://bioservices.usd.edu/bioextract/help/BioExtractServerUserManual.pdf https://www.bioextract.org/query/index.jsp FASTA format
Bioinformatic Harvester defunct bioinformatic meta search engine http://harvester.kit.edu
BioJS open-source library of JavaScript components to visualise biological data Apache License JavaScript http://biojs.net
BioLinux software
BioModels Database database of biological reactions CC0 European Bioinformatics Institute
Babraham Institute
California Institute of Technology
http://www.ebi.ac.uk/biomodels-main/
BioNumerics software for Microsoft Windows Applied Maths Microsoft Windows http://www.applied-maths.com
BioPerl software, from 2002 Artistic License 1.7.6 Perl https://bioperl.org
BioPHP software PHP http://biophp.org/
Biopython collection of open-source tools for computational biology Python http://biopython.org
Blast2GO bioinformatics platform for high-quality functional annotation and analysis of genomic datasets BioBam Bioinformatics Java http://www.blast2go.de
BLAT pairwise sequence alignment algorithm Jim Kent https://genome.ucsc.edu/goldenPath/help/blatSpec.html http://genome.ucsc.edu
BNAber integrated web resource focused on maintaining a comprehensive database of broadly neutralizing HIV-1 antibodies Sanford Burnham Prebys Medical Discovery Institute http://www.bnaber.org/
Budapest Reference Connectome parametrizable consensus brain graph Perl http://pitgroup.org/connectome/
C3D software for geometric modeling ASCON C++ Microsoft Windows
CADEC software application that performs composite materials analysis http://help.cadec-online.com/UserManualEN/ http://cadec-online.com
Cambridge Algebra System computer algebra system Stephen R. Bourne
John Fitch
ALGOL 68C
BCPL
Car–Parrinello molecular dynamics computational chemistry software package
CARET software http://brainvis.wustl.edu/ NII
Cartopedia atlas computer program
CASINO quantum Monte Carlo program Theory of Condensed Matter group http://www.tcm.phy.cam.ac.uk/~mdt26/casino_manual_dir/casino_manual.pdf https://vallico.net/casinoqmc/
CASTEP density functional theory software Theory of Condensed Matter group Fortran http://www.castep.org/
CASTp software http://sts-fw.bioengr.uic.edu/castp/index.php Protein Data Bank
CFD-ACE+ commercial computational fluid dynamics solver ESI Group
CFD-FASTRAN Computational Fluid Dynamics software package ESI Group https://www.esi-group.com/software-solutions/virtual-environment/cfd-multiphysics/ace-suite/cfd-fastran
ChemDraw software for chemical structure drawing PerkinElmer macOS
Microsoft Windows
iOS
https://www.cambridgesoft.com/ CDX Format
CDXML
MDL Molfile
Structure-data file
ChemDraw file
ChemDraw file
Chemical WorkBench software
ChemWindow chemical structure drawing and publishing program Bio-Rad Laboratories http://www.bio-rad.com/en-us/product/chemical-structure-drawing-software?pcp_loc=catprod CDX Format
MDL Molfile
CIP-Tool software tool for the modeling and implementation of event-driven applications ETH Zurich http://www.actifsource.com/solutions/cip_tool/
Citavi software for reference management and knowledge organization proprietary license 6.1 Microsoft Windows http://www.citavi.com
Clever bot web application Rollo Carpenter http://www.cleverbot.com/
Clone manager bioinformatics software http://www.scied.com/pr_cmpro.htm
CloudSim software Java http://www.cloudbus.org/cloudsim/
Code V software for the design and analysis of optical imaging and optical communication systems proprietary license Synopsys https://optics.synopsys.com/codev/
CodonCode Aligner software for DNA sequence assembly, sequence alignment, and editing proprietary license macOS
Microsoft Windows
http://www.codoncode.com/aligner AB1 file format
SCF
FASTA format
FASTQ format
GenBank file format
EMBL file format
SCF
FASTA format
FASTQ format
Nexus file
PHYLIP file format
COGO suite of programs used in civil engineering https://www.cogosoftware.com/
COLUMBUS computational chemistry software suite
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis cloud computing service http://www.camera.calit2.net/
Community Earth System Model numerical simulation of Earth systems National Center for Atmospheric Research https://www.cesm.ucar.edu/
CompHEP software package for automatic computations in High Energy Physics non-commercial 4.5.2rc SINP MSU https://theory.sinp.msu.ru/dokuwiki/lib/exe/fetch.php/comphep/manual-3.3.pdf http://comphep.sinp.msu.ru/
CompuCell3D C++ software problem solving environment for simulations of biocomplexity problems C++ http://www.compucell3d.org/Manuals http://www.compucell3d.org/
Computational Resource for Drug Discovery computational resources for drug design
Computer assisted qualitative data analysis software software
COmputer STored Ambulatory Record software for electronic medical records Massachusetts General Hospital
CONQUEST linear scaling, or O(N), density functional theory (DFT) electronic structure code for modelling atom structures
Consed program for viewing, editing, and finishing DNA sequence assemblies David Gordon C++ Linux
macOS
http://bozeman.mbt.washington.edu/consed/consed.html
CoNTub software for generating 3D structures of arbitrary carbon nanotube connections freeware Java Virtual Machine Java http://www.ugr.es/local/gmdm/contub.htm
CORSIKA physics software https://web.ikp.kit.edu/corsika/usersguide/usersguide.pdf https://www.ikp.kit.edu/corsika/
CPCe Windows-based software
CricketGraph legacy graphics software for Apple Macintosh Apple Macintosh
Crucible software
CS23D web server to generate 3D structural models from NMR chemical shifts University of Alberta http://www.cs23d.ca/index.php
Dalton ab initio quantum chemistry computer program http://daltonprogram.org/www/resources/dalton2016manual.pdf http://daltonprogram.org/
Dashboard of Sustainability software package configured to convey the complex relationships among economic, social, and environmental issues
Datacopia software for making charts and infographics http://www.datacopia.com/ comma-separated values
tab-separated values
text file
DataDetective data mining platform Sentient Information Systems
Dataplot software system for scientific visualization, statistical analysis, and non-linear modeling National Institute of Standards and Technology Fortran GNU/Linux
Unix
macOS
Microsoft Windows
http://www.itl.nist.gov/div898/software/dataplot/refman1/homepage.htm http://www.itl.nist.gov/div898/software/dataplot/index.htm
DataScene software for graphing, animation, data analysis, and real-time data monitoring GNU/Linux
Microsoft Windows
Unix
http://www.cyber-wit.com/
DAVID online bioinformatics resource freeware https://david.ncifcrf.gov/content.jsp?file=functional_annotation.html http://david.abcc.ncifcrf.gov/home.jsp
Dedoose software http://www.dedoose.com
Deep-Sky Planner software for Microsoft Windows Microsoft Windows
Delaunay tessellation field estimator software
Desmos browser-based graphing calculator Desmos https://www.desmos.com/
DialogOS graphical programming environment for dialog design http://www.clt-st.de/produkte-losungen/dialogos/
Dialogue-Assisted Visual Environment for Geoinformation gesture and voice interface for GIS Pennsylvania State University
Diffpack programming environment for developing simulation software Hans Petter Langtangen C++
Python
Perl
Microsoft Windows
GNU/Linux
macOS
Unix
http://www.diffpack.com/diffpack_reference/ http://www.diffpack.com
Dipmeter Advisor expert system for oil exploration data Schlumberger Interlisp
Dirac ab initio quantum chemistry program GNU/Linux
Unix
macOS
Microsoft Windows
http://www.diracprogram.org/doc/release-16/ http://www.diracprogram.org/doku.php XYZ file format
Discovery Studio molecular modeling software Accelrys SUSE Linux Enterprise Server http://accelrys.com/products/collaborative-science/biovia-discovery-studio/ Protein Data Bank
Chemical table file
MDL Molfile
DISLIN software C
FORTRAN 77
Fortran 90
Microsoft Windows
Linux
Unix
OpenVMS
MS-DOS
macOS
http://www.mps.mpg.de/dislin/online-manual http://www.dislin.de/
Distributed Oceanographic Data Systems software National Oceanic and Atmospheric Administration http://dods.ndbc.noaa.gov/
DMol3 software package used to calculate the electronic properties of molecules, clusters, surfaces and crystalline solid materials
DoctorBase business and software, from 2010 http://www.doctorbase.com
DP code software package for physics http://www.dp-code.org/
Dr. Sbaitso artificial intelligence speech synthesis program Creative Technology Disk Operating System
DrawMD patient education software http://www.drawmd.com/
Drug Design and Optimization Lab distributed computing project for discovering drug candidates
Drugfire multimedia database imaging system
DXplain clinical decision support system Massachusetts General Hospital http://www.mghlcs.org/projects/dxplain
Earth Simulator highly parallel vector supercomputer system for running global climate models NEC
Earth System Grid data distribution portal
EarthBrowser virtual globe software http://www.earthbrowser.com/
Eccky life simulation game
ECLIPSE oil and gas reservoir simulator Schlumberger https://www.software.slb.com/products/eclipse
Ecodrive automotive software Microsoft
Fiat
http://ecodrive.driveuconnect.eu/
EcosimPro simulation tool for modelling simple and complex physical processes Microsoft Windows http://www.ecosimpro.com
EditGrid Web 2.0 spreadsheet service Team and Concepts http://www.editgrid.com/
EGS software for simulating radiation therapy sources SLAC National Accelerator Laboratory
eMovie plug-in for PyMOL to make molecular movies
Empire computer program
EnABLE software history matching and uncertainty assessment software for the oil and gas industry http://www.emerson.com/en-us/automation/roxar
Engineering Equation Solver general equation-solving program http://www.fchart.com/ees/
Enterprise Dynamics software proprietary license Delphi
C++
Microsoft Windows http://www.incontrolsim.com/product/enterprise-dynamics/
Epi Map mapping module for Epi Info public domain Centers for Disease Control and Prevention Visual Basic Microsoft Windows http://www.cdc.gov/EpiInfo/
ESMF earth science software https://www.earthsystemcog.org/projects/esmf/
ESTAR software for robotic telescopes University of Exeter
Liverpool John Moores University
ETAP-3 linguistic processing system http://cl.iitp.ru/etap
eTBLAST free text similarity service search engine
Eurisko software Douglas B. Lenat
EXCITING software http://exciting-code.org/
Extensible Computational Chemistry Environment problem-solving environment for computational chemistry Pacific Northwest National Laboratory Linux http://ecce.emsl.pnl.gov/
FastPCR software tool for the design of PCR primers and probes http://primerdigital.com/fastpcr/m1.html http://primerdigital.com/fastpcr.html text file
Rich Text Format
FASTA format
FDMNES physics software http://neel.cnrs.fr/spip.php?rubrique1007&lang=fr
FEFF physics software Fortran http://monalisa.phys.washington.edu/feffproject-feff.html
FitIt software to fit spectra using multidimensional interpolation approximation http://www.nano.sfedu.ru/research/projects/fitit/
Flexpde partial differential equations software http://www.pdesolutions.com/help/index.html http://www.pdesolutions.com/ Drawing Interchange Format
Wavefront .obj file
FlexPro software package for analysis and presentation of scientific and technical data proprietary license 11.0.8 http://www.weisang.com/ NetCDF
ASAM MDF
Compound File Binary File Format
comma-separated values
Common Data Format
Hierarchical Data Format
binary file
HyperText Markup Language
Waveform Audio File Format
Compound File Binary File Format
comma-separated values
Common Data Format
Flood Modeller Pro software that simulates the flow of water through river channels and across floodplains CH2M Hill C# http://help.floodmodeller.com/floodmodeller/ https://www.floodmodeller.com
FlowJo software package for analyzing flow cytometry data https://www.flowjo.com/
FLUKA monte carlo simulation software proprietary license 2011.2c.0 Istituto Nazionale di Fisica Nucleare Fortran Linux http://www.fluka.org/content/manuals/FM.pdf http://www.fluka.org/
FlyExpress database that collects the expression patterns of Drosophila melanogaster in embryogenesis freeware Biodesign Institute http://www.flyexpress.net
FoldX protein design software http://foldxsuite.crg.eu/documentation#manual http://foldxsuite.crg.eu/
FORDISC software for forensic anthropology http://fac.utk.edu/fordisc-3-1-personal-computer-forensic-discriminant-functions/
formatdb discontinued software tool for molecular bioinformatics
Framsticks software for simulation of artificial life http://www.framsticks.com/files/common/Framsticks_Manual.pdf http://www.framsticks.com/
FreeFlyer software application for use in satellite mission analysis, design and operations a.i. solutions Microsoft Windows http://www.ai-solutions.com/ProductsServices/FreeFlyer/Overview.aspx
Fusionviewer medical image display software package http://fusionviewer.sourceforge.net/docs/FusionViewerUsersGuide.pdf Portable Network Graphics
Tagged Image File Format
JPEG File Interchange Format
Windows Bitmap
Digital Imaging and Communications in Medicine
Gene Designer software for gene design freeware Microsoft Windows http://www.dna20.com/resources/genedesigner
GeneMark gene prediction software Georgia Institute of Technology Linux
macOS
http://opal.biology.gatech.edu/GeneMark/
http://opal.biology.gatech.edu/GeneMark
GenePattern genomic data analysis software Broad Institute http://software.broadinstitute.org/cancer/software/genepattern/user-guide http://www.genepattern.org
GENSCAN software program to identify complete gene structures in genomic DNA Christopher Burge http://genes.mit.edu/GENSCANinfo.html
Geomodeller3D software tool for 3D geologic modelling http://www.geomodeller.com/
GeoXACML geo extension for XACML http://geoxacml.secure-dimensions.com/
GESS software for analyzing gene expression data obtained from microarrays http://www.ncss.com/
GEUP geometry software for interactive math visualization Windows 10
Windows 8.1
Windows 8
Windows 7
Windows Vista
Windows XP
Windows 2000
Windows NT 4.0
Windows Me
Windows 98
Windows 95
http://www.geup.net/geup7_quickguide.pdf http://www.geup.net/
Geworkbench open-source software platform for integrated genomic data analysis open source license Columbia University Java Microsoft Windows http://www.geworkbench.org Affymetrix CEL Data File Format
FASTA format
Protein Data Bank
GMS software for building and simulating groundwater models Aquaveo http://aquaveo.com/software/gms-groundwater-modeling-system-introduction ADRG General Information File
ARC Standard Raster Product
Band Interleaved by Line Image File
BigTIFF
Compressed ARC Digitized Raster Graphics
ERDAS Imagine IMG
GRIB
GeoPDF
JP2
MrSID
National Imagery Transmission Format Standard
Keyhole Markup Language Zipped
PCX
Portable Graymap, text variant
Portable Network Graphics
GeoTIFF
Digital orthophoto quadrangle
Digital raster graphic
MapInfo Interchange Format
ZoomifyImageFormat
LAS file format
dBASE Table File Format
E57 Lidar Point Cloud Format
SOSI
GoldSim software for Microsoft Windows Microsoft Windows http://www.goldsim.com
Google Sky Feature for Google Earth and an online sky/outer space viewer at www.google.com/sky. http://www.google.com/sky
GoTo type of telescope mount and related software
GPOPS-II software for macOS macOS http://gpops2.com
GRAPE software for for mathematical visualization University of Freiburg
University of Bonn
https://archive.ins.uni-bonn.de/numod.ins.uni-bonn.de/grape/MANUAL/manual/manual.html http://numod.ins.uni-bonn.de/grape/
Grapher graphing calculator software Apple Inc. Encapsulated PostScript
Portable Document Format
QuickTime File Format
Graphmatica equation plotter with numerical and calculus features macOS
Microsoft Windows
iOS
http://www.graphmatica.com/
GraphPad InStat statistical analysis software GraphPad Software Microsoft Windows
macOS
http://www.graphpad.com/instat Windows Metafile
PICT
GraphPad Prism 2D graphing and statistics software GraphPad Software macOS
Microsoft Windows
http://www.graphpad.com/guides/prism/7/user-guide/ http://www.graphpad.com/
http://www.graphpad.com/prism
GraphPad Prism file format
GraphPad Prism file format, version 4
GraphPad Prism file format
GraphPad Prism file format, version 4
groundwater model type of scientific model
GSI3D software
GYRO Physics software General Atomics https://fusion.gat.com/theory/Gyrogeometry https://fusion.gat.com/theory/Gyro
Handel software for multiple sequence alignment C++ http://biowiki.org/HANDEL
HAZUS software tool for natural hazard analysis Federal Emergency Management Agency Windows 10
Windows 8.1
Windows 7
https://www.fema.gov/hazus/
HDF Explorer data visualization program Microsoft Windows http://www.space-research.org/ Hierarchical Data Format
NetCDF
HEC-RAS software for modeling the hydraulics of water flow freeware 4.1 United States Army Corps of Engineers Windows XP
Windows Vista
Windows 7
Windows 8
Windows 8.1
Windows 10
http://www.hec.usace.army.mil/software/hec-ras/documentation/HEC-RAS%205.0%20Users%20Manual.pdf http://www.hec.usace.army.mil/software/hec-ras
HemoSpat bloodstain pattern analysis software C++ macOS
Windows 7
Windows 8
Windows 8.1
Windows 10
http://hemospat.com comma-separated values
Digital Asset Exchange
Drawing Interchange Format
Wavefront .obj file
Virtual Reality Modeling Language
HipNav computer-assisted surgery system Carnegie Mellon University
HNSKY night sky simulator software freeware Microsoft Windows
GNU/Linux
http://www.hnsky.org/help/uk/hnsky.htm http://www.hnsky.org/software.htm
HTK Hidden Markov Model software proprietary license Cambridge University Engineering Department GNU/Linux
Microsoft Windows
macOS
http://htk.eng.cam.ac.uk/
Huygens Suite image processing software tools https://svi.nl/HomePage
HyperRESEARCH qualitative data analysis software http://www.researchware.com/
HYPHY computational phylogenetics software http://www.hyphy.org/
I-TASSER software for for protein structure prediction and refinement, and structure-based protein function annotations http://zhanglab.ccmb.med.umich.edu/I-TASSER/
iDPS Software graphics server software
Illyria software Common Lisp
Image Studio Lite software for Western blot analysis LI-COR Biosciences Java macOS Sierra
Windows 10
http://www.licor.com/bio/products/software/image_studio_lite/ JPEG File Interchange Format
Portable Network Graphics
Tagged Image File Format
imc FAMOS software for the analysis, visualization and documentation of measurement data http://www.imc-famos.de
http://www.imcfamos.com/
Integrated Ballistics Identification System software for firearm identification
Integrated Software for Imagers and Spectrometers digital image processing software public domain United States Geological Survey C++ Ubuntu
Red Hat Enterprise Linux
Debian
Fedora
macOS
https://isis.astrogeology.usgs.gov/Application/index.html http://isis.astrogeology.usgs.gov
Intel Array Visualizer software Polygon File Format
Internist-I computer-assisted diagnostic software tool University of Pittsburgh
IRAF software system for the reduction and analysis of astronomical data Java 5 National Optical Astronomy Observatory http://iraf.noao.edu
IRAP RMS Suite reservoir characterization and modeling software Roxar AS Linux http://www.roxarsoftware.com
http://www.emerson.com/en-us/automation/operations-business-management/reservoir-management-software
iRows defunct web-based spreadsheet software
ISIS/Draw chemical structure drawing software for Windows MDL Information Systems http://accelrys.com/products/informatics/cheminformatics/draw/index.html
Jalview software for multiple sequence alignment editing, visualization and analysis Andrew Waterhouse
James Cuff
http://www.jalview.org/version118/documentation.html http://www.jalview.org General feature format
FASTA format
Clustal file format
JME Molecule Editor molecule editor Java applet Comenius University in Bratislava Java http://www.molinspiration.com/jme Simplified molecular input line entry specification
Jpred protein secondary structure prediction server http://www.compbio.dundee.ac.uk/jpred4/about.shtml
JUICE software for editing and analyses of phytosociological data Masaryk University http://www.sci.muni.cz/botany/juice/
KANT computer algebra software Technical University of Berlin GNU/Linux
macOS
Microsoft Windows
http://page.math.tu-berlin.de/~kant/KASH/pdf/kash3intro.pdf http://www.math.tu-berlin.de/~kant/kash.html
Kekulé Program chemistry software
Kepler scientific workflow system software application for analyzing and modeling scientific data Berkeley Software Distribution R University of California, Davis
University of California, Santa Barbara
University of California, San Diego
Java Microsoft Windows
macOS
GNU/Linux
https://code.kepler-project.org/code/kepler-docs/trunk/outreach/documentation/shipping/2.5/UserManual.pdf https://kepler-project.org/
KiSAO ontology and software http://co.mbine.org/standards/kisao
KIVA Computational Fluid Dynamics software Los Alamos National Laboratory Fortran
Fortran 95
http://www.lanl.gov/projects/feynman-center/deploying-innovation/intellectual-property/software-tools/kiva/index.php
Laboratory Unit for Computer Assisted Surgery for virtual surgical planning
LandView viewer for GIS data United States Census Bureau https://www.census.gov/geo/landview/
Language Acquisition Device computer program, software, and language acquisition device King's College London
Lead Finder software
LISE++ spectrometry software freeware C++ http://lise.nscl.msu.edu
LONI Pipeline scientific workflow software freeware Java Runtime Environment Java Linux
macOS
Microsoft Windows
http://pipeline.loni.usc.edu/learn/user-guide/ http://pipeline.loni.usc.edu/
MacVector molecular biology software proprietary license MacVector macOS http://www.macvector.com
Maestro publicly available version of the software used by the NASA Mars Exploration Rover team Jet Propulsion Laboratory Java GNU/Linux
Mac OS X Panther
Windows XP
Windows 2000
https://mars.nasa.gov/mer/relatedsites/
MAFFT multiple alignment software for amino acid or nucleotide sequences Berkeley Software Distribution macOS
Microsoft Windows
GNU/Linux
http://mafft.cbrc.jp/alignment/software/
MapleSim multi-domain modeling and simulation software proprietary license Waterloo Maple http://www.maplesoft.com/products/maplesim/index.aspx
Mars regional atmospheric modeling system software that simulates the circulations of the Martian atmosphere http://www.boulder.swri.edu/~rafkin/
Mascot software that uses mass spectrometry data to identify proteins from peptide sequence databases Linux http://www.matrixscience.com/
MassMatrix data analysis software proprietary software license http://www.massmatrix.bio/wp-content/uploads/2015/02/MassMatrix_PC_GUI_Manual.pdf http://www.massmatrix.bio/
MasterPlex QT curve-fitting software proprietary software license Hitachi Software Engineering https://psg.hitachi-solutions.com/masterplex
MasterPlex ReaderFit software proprietary license Hitachi Software Engineering http://www.MiraiBio.com/Elisa-Curve-Fit
Math-o-mir software tool for mathematical equations MIT license C++ Windows 2000
Windows XP
Windows Vista
Windows 7
Windows 8
Windows 10
http://gorupec.awardspace.com/MathomirManual.pdf http://gorupec.awardspace.com/mathomir.html
MathMagic software for editing mathematical equations Microsoft Windows
macOS
Android
iOS
http://www.mathmagic.com
MAXQDA software program designed for computer-assisted qualitative and mixed methods data, text and multimedia analysis in academic, scientific, and business institutions proprietary software license http://www.maxqda.com/download/manuals/MAX12_manual_eng.pdf http://www.maxqda.com/ M2k
Binary Interchange File Format
Office Open XML file formats
Advanced Video Coding
QuickTime File Format
MPEG program stream
Audio Video Interleave, version 1.22.0
M4V
3GP and 3G2
Windows Media Video
Portable Document Format
Microsoft Word Binary File Format
OpenDocument Text, version 1.0
Rich Text Format
Statistical Package for the Social Sciences data file
SubRip
RIS
plain text
M2k
MedCalc statistical software proprietary software license https://www.medcalc.org/manual/index.php https://www.medcalc.org/ Office Open XML Spreadsheet Document, Transitional, ISO/IEC 29500:2008
OpenDocument Spreadsheet, version 1.0
dBASE Table File Format
text file
Data Interchange Format
MEGAN metagenomic analysis software Java http://ab.inf.uni-tuebingen.de/software/megan6/
MELCOR software Sandia National Laboratories http://energy.sandia.gov/energy/nuclear-energy/nuclear-energy-safety-technologies/melcor/
MEME suite software tools for the discovery and analysis of sequence motifs National Institutes of Health http://meme-suite.org/ FASTA format
Clustal W
Mercury crystallography software Cambridge Crystallographic Data Centre Windows 7
Windows 8
Windows 10
GNU/Linux
macOS
https://www.ccdc.cam.ac.uk/solutions/csd-system/components/mercury/
Metascape gene annotation and analysis software freeware GNF http://metascape.org
MeVisLab cross-platform application framework for medical image processing and scientific visualization proprietary software license 2.7
2.7.1
2.8.1
MeVis Medical Solutions C++ http://www.mevislab.de/
Mind's Eye video analysis software http://www.darpa.mil/Our_Work/I2O/Programs/Minds_Eye.aspx
MLwiN statistical software University of Bristol http://www.bristol.ac.uk/cmm/software/mlwin/download/manuals.html http://www.bristol.ac.uk/cmm/software/mlwin/
MochiView genomic sequence browsing software University of California, San Francisco Java http://www.johnsonlab.ucsf.edu/s/MochiView_Manual_v145.pdf http://www.johnsonlab.ucsf.edu/mochi/
Mocolo video analysis software
Model for Prediction Across Scales simulation software National Center for Atmospheric Research https://mpas-dev.github.io/
MODELLER software for homology modeling University of California, San Francisco Microsoft Windows
macOS
GNU/Linux
Unix
https://salilab.org/modeller/manual/ https://salilab.org/modeller/
Molden molecular and electronic structure software Center for Molecular and Biomolecular Informatics Microsoft Windows
Linux
macOS
IRIX
SunOS
Solaris
http://cheminf.cmbi.ru.nl/molden/ Protein Data Bank
Molden format
Molden format
Molecular Evolutionary Genetics Analysis software for statistical analysis of molecular evolution Pennsylvania State University http://www.megasoftware.net/web_help_7/helpfile.htm#hc_first_time_user.htm http://www.megasoftware.net
MolIDE software for comparative modeling of protein structures Fox Chase Cancer Center
Monte Carlo N-Particle Transport Code software package for simulating nuclear processes Los Alamos National Laboratory Fortran https://laws.lanl.gov/vhosts/mcnp.lanl.gov/mcnp_manual.shtml http://mcnpx.lanl.gov/
https://mcnp.lanl.gov
Moog astronomical software package Fortran http://www.as.utexas.edu/~chris/moog.html
Morphobank web application for collaborative evolutionary research https://morphobank.org/themes/default/graphics/pdf/quick_start_guide.pdf https://morphobank.org/
MountainsMap micro-topography software published by Digital Surf Digital Surf Microsoft Windows http://www.digitalsurf.com/en/mntkey.html
http://www.digitalsurf.fr/en/platform0.html
text file
Windows Bitmap
JPEG File Interchange Format
Tagged Image File Format
Portable Network Graphics
3D Manufacturing Format
Virtual Reality Modeling Language
STereoLithography
MovAlyzeR software package for handwriting movement analysis C++ http://www.neuroscript.net/help/webframe.html http://www.neuroscript.net/movalyzer.php
MUMmer software for sequence alignment Artistic License C
C++
http://mummer.sourceforge.net/manual/ http://mummer.sourceforge.net/
MUSCLE sequence alignment software public domain software C++ http://www.drive5.com/muscle FASTA format FASTA format
PHYLIP file format
Mycin early expert system with a focus on medical research
MyDirectives digital cloud-based advance medical directives platform
NAMD molecular dynamics simulation software 2.10 University of Illinois at Urbana–Champaign C++ http://www.ks.uiuc.edu/Research/namd/current/ug/ http://www.ks.uiuc.edu/Research/namd
NanoLanguage simulation software for nanoscale systems
National Integrated Ballistic Identification Network software in United States of America, from 1999
Naval Observatory Vector Astrometry Subroutines software United States Naval Observatory C http://aa.usno.navy.mil/software/novas/novas_info.php
NAVGEM global numerical weather prediction computer simulation
NCSS statistical software https://www.ncss.com/software/ncss/ncss-documentation/ http://www.ncss.com/software/ncss ACCDB File Format Family
dBASE Table File Format
Office Open XML Spreadsheet Document, ECMA-376 1st Edition
MATLAB M-File
R Data Format Family
NEMO astronomy software 3.3.2 C
Fortran
C++
http://admit.astro.umd.edu/nemo/manual/nemo.html http://admit.astro.umd.edu/nemo/
Neuro Laboratory software, from 2006 http://www.scientific-soft.com/
Newbler software package for de novo DNA sequence assembly 454 Life Sciences Linux FASTA format
FASTQ format
NICMOSlook software to analyze spectral data obtained with the NICMOS spectrometer Space Telescope European Coordinating Facility Interactive Data Language
NinJo meteorological software Deutscher Wetterdienst
Meteorological Service of Canada
Danish Meteorological Institute
Federal Office of Meteorology and Climatology MeteoSwiss
Bundeswehr
GNU/Linux
Microsoft Windows
http://www.ninjo-workstation.com/
NLPQLP Fortran subroutine that solves smooth nonlinear programming problems
Nmrpipe data processing software for nuclear magnetic resonance https://www.ibbr.umd.edu/nmrpipe/install.html
NNPDF software http://nnpdf.hepforge.org
NoeClone software http://www.noegen.com
NONMEM software for population pharmacokinetic modeling University of California, San Francisco https://nonmem.iconplc.com/nonmem710/intro7.pdf
NPSOL software package for solving constrained optimization problems proprietary license Fortran http://www.ccom.ucsd.edu/~peg/papers/npdoc.pdf http://www.sbsi-sol-optimize.com/asp/sol_product_npsol.htm
NuCalc graphing calculator software Microsoft Windows
macOS
iOS
http://www.pacifict.com
http://www.pacifict.com/
NUKEMAP unclassified nuclear weapons effects data map software Alex Wellerstein http://www.nuclearsecrecy.com/nukemap/
OE-Cake! 2D fluid physics sandbox software Microsoft Windows http://www.prometech.co.jp/
OELib cheminiformatics software library C++
OLGA software modelling tool for transportation of oil, natural gas and water in the same pipeline proprietary license Equinor
SINTEF
https://www.software.slb.com/products/olga
OLI Analyzer software used for simulating aqueous-based chemical systems proprietary license https://www.olisystems.com/oli-studio-analyzers-scalechem
OLIGO Primer Analysis Software tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes Microsoft Windows
macOS
http://oligo.net/oligo_7_manual.pdf
http://www.oligo.net/oligo_7_manual.pdf
http://oligo.net/
Openlab software for 2D microscope image processing proprietary license http://www.icd.eu/produkte/openlab-cds.html
Optica Optics Software optical design software program http://www.opticasoftware.com/
Origin scientific graphing and data analysis software by OriginLab Corporation proprietary license 2017 SR2 Microsoft Windows http://www.originlab.com
ORTEP computer program and software Oak Ridge National Laboratory
Orthopaedic Studio software for quantitative hip examinations OsiriX http://orthostudio.spectronic.se
Osteoware data recording software for human skeletal material http://osteoware.si.edu/
Overflow fluid dynamics simulation software https://overflow.larc.nasa.gov/home/users-manual-for-overflow-2-2/ https://overflow.larc.nasa.gov
Parasurf molecular modelling software Linux http://www.ceposinsilico.de/pdf/ParaSurf12.pdf http://www.ceposinsilico.de/products/parasurf.htm
PARATEC physics software Lawrence Berkeley National Laboratory http://www.nersc.gov/users/software/applications/materials-science/paratec/
PASS Sample Size Software sample size software tools proprietary license NCSS Microsoft Windows http://www.ncss.com/
https://www.ncss.com/software/pass/
PatternHunter homology search instrument software
PDBREPORT database of anomalies and errors in Protein Data Bank http://swift.cmbi.ru.nl/gv/pdbreport
PeakFit automated nonlinear peak separation and analysis software package proprietary license Microsoft Windows http://www.systat.com/products/PeakFit/
Petrel software for exploration of petroleum and gas reserves proprietary software Schlumberger
PhotoModeler stereophotogrammetry software proprietary license http://www.photomodeler.com JPEG File Interchange Format
Tagged Image File Format
Windows Bitmap
PCX
Truevision TGA
Portable Network Graphics
PICT
Photoshop File Format
Portable Pixmap, text variant
MacPaint
Interchange File Format
CALS Raster file format
Photo CD
Silicon Graphics Image
JP2
HD Photo
QuickTime File Format
MPEG-4 Part 14
Audio Video Interleave, version 1.22.0
Windows Media Video
3GP and 3G2
MPEG-1 program stream
Drawing Interchange Format
Wavefront .obj file
3D Studio mesh-file format
comma-separated values
3D Studio mesh-file format
Rhino 3D Model
comma-separated values
Drawing Interchange Format
Filmbox
Initial Graphics Exchange Specification
Keyhole Markup Language
Keyhole Markup Language Zipped
LAS file format
Wavefront .obj file
Recon Points
STereoLithography
Virtual Reality Modeling Language
Phrap software for DNA sequence assembly Philip Palmer Green C macOS
Berkeley Software Distribution
HP-UX
Tru64 UNIX
IBM AIX
Linux
Microsoft Windows
IRIX
Solaris
http://bozeman.mbt.washington.edu/consed/consed.html
Phred base calling software for DNA sequencing analysis Philip Palmer Green C macOS
Berkeley Software Distribution
HP-UX
Tru64 UNIX
IBM AIX
Linux
Microsoft Windows
IRIX
Solaris
http://www.phrap.com/phred/
Phylogenetic Analysis Using Parsimony *and other methods software http://paup.csit.fsu.edu/ Nexus file
Phyloscan software for sequence motifs in intergenic regions Wadsworth Center
New York State Department of Health
http://ccmbweb.ccv.brown.edu/cgi-bin/phyloscanV2.pl
PhyloXML XML language for the analysis, exchange, and storage of phylogenetic trees http://www.phyloxml.org/
Phyre / Phyre2 software for protein structure prediction http://www.sbg.bio.ic.ac.uk/phyre2
Physicians' Information and Education Resource software http://pier.acponline.org
PicoScope oscilloscope software application proprietary software Pico Technology Visual C++ Microsoft Windows
macOS
Debian
Ubuntu
PiHex software for calculating the bits of Pi
PLINK whole genome association analysis toolset C
C++
http://zzz.bwh.harvard.edu/plink/
Plotly online analytics and data visualization tool https://plot.ly/
PowerLab software ADInstruments
Predictor@home citizen science project
Prime95 software for finding Mersenne primes freeware 29.8 build 3 George Woltman C
x86 assembly language
https://mersenne.org/download
Primer Premier software for the design and analysis of PCR primers Premier Biosoft http://www.premierbiosoft.com
http://www.premierbiosoft.com/primerdesign/index.html
PrimerPlex software for designing primers for multiplex PCR Premier Biosoft Microsoft Windows
Apple Macintosh
http://www.premierbiosoft.com
http://www.premierbiosoft.com/primerplex/index.html
Primou software
PROLITH photolithography simulation software Chris Mack https://www.kla-tencor.com/Virtual-Lithography/dsmprolith.html
Promine mining and geology software http://www.promine.com
ProStat statistical software Windows 98
Windows Vista
Windows 7
Windows 8
http://www.polysoftware.com/index.htm ASCII
dBASE Table File Format
Data Interchange Format
comma-separated values
ASCII
dBASE Table File Format
Data Interchange Format
Protomap proteomics software Benjamin Cravatt III http://www.scripps.edu/cravatt/protomap/
PSF Lab microscope software freeware http://onemolecule.chem.uwm.edu/software
PSI Protein Classifier software
PSI-Plot data analysis and technical plotting software http://www.polysoftware.com/psiplot.htm
PSIPRED software for Windows 2000 University College London C Windows 2000 http://bioinf.cs.ucl.ac.uk/psipred/
PSORT bioinformatics software
Psychtoolbox for MATLAB software http://psychtoolbox.org/
PupaSuite web-based SNP analysis tool
Pwpaw software http://users.wfu.edu/natalie/papers/pwpaw/man.html
PyQuante software http://pyquante.sourceforge.net/
PYTHIA computer simulation program 8.205 Lund University C++ http://www.thep.lu.se/~torbjorn/Pythia.html
Q-systems software
QDA Miner qualitative data analysis software Provalis Research Microsoft Windows http://www.provalisresearch.com/
Quickfield finite element analysis software package Microsoft Windows http://www.quickfield.com/
RadExPro seismic software seismic processing software Microsoft Windows
RAPTOR protein threading software Microsoft Windows
Linux
http://www.bioinfor.com/raptor
RaptorX software for protein modeling and analysis http://raptorx.uchicago.edu/
RealSky digital photographic sky atlas
Redcap Research Electronic Data Capture end-user license agreement PHP https://www.project-redcap.org/
RedShift planetarium software created by Maris Multimedia https://www.redshift-live.com/ext/en/
RefDB NMR spectroscopy database of carefully corrected or re-referenced chemical shifts http://refdb.wishartlab.com/
Regional Atmospheric Modeling System software William R. Cotton
Roger A. Pielke
http://www.atmet.com/html/docs/rams/rams_techman.pdf http://rams.atmos.colostate.edu/detailed.html
Registax image processing software for amateur astrophotographers freeware Microsoft Windows http://www.astronomie.be/registax
RELAP5-3D 1997 software, from 1997 Idaho National Laboratory Fortran http://www.inl.gov/relap5/
RMCProfile Reverse Monte Carlo for crystalline and disordered materials Oak Ridge National Laboratory
National Institute of Standards and Technology
University of Cambridge
University of Oxford
http://www.rmcprofile.org/Main_Page
RoboGEO geocoding software program http://robogeo.com/home/
RobotML XML-based markup language that is used for communication between autonomous mobile robots and robot components Munich University of Applied Sciences
Rosalind platform and web project for learning bioinformatics through problem solving http://rosalind.info/problems/locations/
RunGEM software Gempack http://www.copsmodels.com/gprgem.htm
RunMC simulation framework https://runmc.hepforge.org/
SageMathCloud web-based cloud computing and course management platform for computational mathematics Python https://cloud.sagemath.com/
SahysMod agricultural software Delphi Microsoft Windows https://www.waterlog.info/pdf/sahysmod.pdf http://www.waterlog.info/sahysmod.htm
SaltMod agricultural software Delphi Microsoft Windows http://www.waterlog.info/saltmod.htm
SciCast collaborative platform for science and technology forecasting George Mason University http://scicast.org
Scigress software for molecular modelling Fujitsu C++ http://www.scigress.com
Seasonal Attribution Project citizen science project
SEQUEST software for Microsoft Windows and Linux Microsoft Windows
Linux
https://assets.thermofisher.com/TFS-Assets/CMD/manuals/Man-XCALI-97160-SEQUEST-331-User-ManXCALI97160-B-EN.pdf http://www.thermo.com/com/cda/product/detail/0,,16483,00.html?CA=bioworks
Serpent computational physics program VTT Technical Research Centre of Finland C http://montecarlo.vtt.fi/download/Serpent_manual.pdf http://montecarlo.vtt.fi/
SESOIL software, from 1981 United States Environmental Protection Agency Fortran
SGS Genesis software for the modelling of mineral resources SGS S.A. http://www.geostat.com/genesis
Shadows software package for the calculation and drawing of sundials and astrolabes Windows 10
Windows 8
Windows 7
Windows Vista
https://www.shadowspro.com/en/user-manual.html https://www.shadowspro.com/en/index.html
SHARC molecular dynamics software molecular dynamics software Fortran Linux http://sharc-md.org/
SHELX set of crystallography programs SHELX-76
SHELX-97
SHELX-2017
George M. Sheldrick http://shelx.uni-goettingen.de/shelxl_user_guide.pdf http://shelx.uni-goettingen.de/ Crystallographic Information File
SHELXL software for the refinement of crystal structures George M. Sheldrick http://shelx.uni-goettingen.de/shelxl_user_guide.pdf http://shelx.uni-goettingen.de/
SHELXT small molecule structure solution program George M. Sheldrick http://shelx.uni-goettingen.de/shelxt_keywords.php
SHIFTCOR biological database and software
Short Oligonucleotide Analysis Package bioinformatics software tools http://soap.genomics.org.cn/
SigmaPlot software package for scientific graphing and data analysis Microsoft Windows http://www.sigmaplot.com/products/sigmaplot/sigmaplot-details.php
https://systatsoftware.com/products/sigmaplot/
text file
comma-separated values
Data Interchange Format
Lotus 1-2-3 Worksheet file format, version 4-5
Statistical Analysis System data set (Windows)
JPEG File Interchange Format
Graphics Interchange Format
Portable Network Graphics
Tagged Image File Format
Windows Bitmap
Windows Metafile
Windows Enhanced Metafile
Portable Document Format
Photoshop File Format
Encapsulated PostScript
SIMAP citizen science project http://cube.univie.ac.at/resources/simap
http://mips.gsf.de/simap/
Simcyp Simulator modelling and simulation platform https://www.certara.com/software/physiologically-based-pharmacokinetic-modeling-and-simulation/simcyp-simulator/?ap%5B0%5D=PBPK
SIMION ion optics simulation program proprietary license Microsoft Windows http://simion.com/
Simmcast object-oriented simulation framework for protocol and network research
Sirius visualization software molecular modelling and analysis system San Diego Supercomputer Center http://sirius.sdsc.edu
Sky Map planetarium software application Apache License 1.9.2 Google Android https://github.com/sky-map-team/stardroid
https://play.google.com/store/apps/details?id=com.google.android.stardroid&hl=en
Skyglobe astronomy program freeware MS-DOS
Microsoft Windows
http://www.adamhome.com/skyglobe.htm
SkyTools observation-planning program for astronomers proprietary license Microsoft Windows http://www.skyhound.com/skytools.html
SMS software for building and simulating surface water models Aquaveo http://aquaveo.com/software/sms-surface-water-modeling-system-introduction
Snack Sound Toolkit software Royal Institute of Technology http://www.speech.kth.se/snack/man/snack2.2/python-man.html http://www.speech.kth.se/snack/ Broadcast Wave Format
Sun Microsystems audio file
Audio Interchange File Format
MPEG-1 Audio Layer III HD
Snagger software program for selecting tag SNPs using pairwise r2 linkage disequilibrium MIT license http://snagger.sourceforge.net/
SNARK software Mozilla Public License SRI International Common Lisp http://www.ai.sri.com/~stickel/snark.html
SnoRNA prediction software software
Soaplab software for Java Virtual Machine European Bioinformatics Institute Java Virtual Machine http://soaplab.sourceforge.net/soaplab1/
SOCET SET software BAE Systems http://www.socetset.com
SOFA astronomy software Fortran
C
http://www.iausofa.org/
Solarsoft software Lockheed Martin http://www.lmsal.com/solarsoft/
Space Telescope Science Data Analysis System astronomical software Space Telescope Science Institute http://www.stsci.edu/institute/software_hardware/stsdas
SPEED2000 software for electromagnetic simulation for the analysis and design of high-speed electronic systems Sigrity http://www.sigrity.com/products/speed2000/spd2k.htm
SplitsTree software Microsoft Windows
Linux
macOS
http://ab.inf.uni-tuebingen.de/software/megan4/download1.0/V1_0/manual.pdf/view http://www.splitstree.org
SRM Engine Suite engineering software proprietary license https://cmclinnovations.com/products/srm/
Starlight Information Visualization System visualization software Pacific Northwest National Laboratory https://starlight.pnnl.gov/
Starlink Project UK astronomical computing project http://starlink.eao.hawaii.edu/starlink
Starmad software for Microsoft Windows Microsoft Windows http://www.ssbv.com/ProductDatasheets/page65/index.html
Starry Night planetarium software http://www.starrynight.com/
Statgraphics software 18.1.05 Microsoft Excel http://statgraphics.com/ StatGraphics Data File
STATISTICA analytics software package 12.6 Dell Inc. x86
x86-64
Microsoft Windows http://www.statsoft.com/ STATISTICA Report File STATISTICA Report File
StatPlus software product for basic univariate and multivariate statistical analysis Microsoft Windows http://www.analystsoft.com/en/products/statplus/
StatXact statistical software package Cytel C Microsoft Windows http://www.cytel.com/software/statxact
Stemloc software for pairwise RNA structural alignment https://biowiki.org/wiki/index.php/Stemloc_Tutorial http://biowiki.org/StemLoc Stockholm format
FASTA format
Stockholm format
Stencil code software
STING software for analysis of the relationship between protein sequence, structure, function, and stability http://www.cbi.cnptia.embrapa.br/SMS
Streamer radiative transfer code http://stratus.ssec.wisc.edu/streamer/userman.pdf http://stratus.ssec.wisc.edu/streamer/
Surface Evolver software for computational fluid dynamics freeware C Linux
Microsoft Windows
macOS
Unix
http://facstaff.susqu.edu/brakke/evolver/downloads/manual270.pdf http://www.susqu.edu/facstaff/b/brakke/evolver/evolver.html Pixar picture
Object File Format
PostScript
Softimage PIC
Surgical segment navigator surgical simulation software Carl Zeiss AG https://marmulla.com/compengl.htm
Sysquake numerical computing software 6.0.1 http://www.calerga.com/products/Sysquake/
Systems Tool Kit astrodynamics computer program from Analytical Graphics, Inc http://www.agi.com/stk
T-REX software for inferencing, validation and visualization of phylogenic trees http://www.trex.uqam.ca/ Newick tree format
TableCurve 2D curve-fitting software http://www.systat.com/products/SigmaPlot/
TableCurve 3D software http://www.systat.com/products/SigmaPlot/
Tanagra machine learning software open source 1.4.50 Lumière University Lyon 2 Delphi Microsoft Windows http://eric.univ-lyon2.fr/~ricco/tanagra/fr/tanagra.html
TaveRNA software Simon Fraser University http://compbio.cs.sfu.ca/taverna
Techlog software for wellbore data analysis http://www.slb.com/Techlog
Tecplot family of visualization & analysis software tools https://www.tecplot.com/
TellStar first graphical astronomy software
The Accelrys Enterprise Platform data management platform
The Geochemist's Workbench software tools for solving problems in aqueous chemistry University of Illinois at Urbana–Champaign Microsoft Windows https://www.gwb.com/pdf/GWB12/GWBessentials.pdf http://www.gwb.com
The Lattice Project volunteer computing project Berkeley Open Infrastructure for Network Computing http://boinc.umiacs.umd.edu/
The Proteolysis Map integrated web resource focused on proteases Sanford Burnham Prebys Medical Discovery Institute http://sonny.burnham.org/proteases/
Theorem Proving System automated theorem proving system for first-order and higher-order logic Carnegie Mellon University Common Lisp http://gtps.math.cmu.edu/tps-etps.ps http://gtps.math.cmu.edu/tps.html
TheSky astronomy software proprietary license Software Bisque http://www.bisque.com
TI InterActive! computer algebra software Texas Instruments http://education.ti.com/educationportal/sites/US/productDetail/us_ti_interactive.html
TimeTree database of times of divergence in the tree of life freeware http://www.timetree.org/
Tinker molecular dynamics simulation software 8.2.1 https://dasher.wustl.edu/tinker/downloads/guide.pdf https://www.tinkertools.org/
TITAN2D geoflow simulation software http://www.gmfg.buffalo.edu
TopFIND knowledgebase of protein termini University of British Columbia http://clipserve.clip.ubc.ca/topfind
TRACE orbit determination program The Aerospace Corporation
TracePro optical engineering software
TRAMO statistical software Bank of Spain http://www.bde.es/webbde/es/secciones/servicio/software/econom.html
Tree puzzle software http://www.tree-puzzle.de/
Treefinder for the likelihood-based reconstruction of phylogenetic trees from molecular sequences Gangolf Jobb http://www.treefinder.de/
Ubuntu-Med software
UCSF Chimera software for visualization and analysis of molecular structures University of California, San Francisco http://www.cgl.ucsf.edu/chimera/index.html
http://www.rbvi.ucsf.edu/chimera/
Protein Data Bank
CCP4
Simplified molecular input line entry specification
XYZ file format
MDL Molfile
Stockholm format
Digital Asset Exchange
Virtual Reality Modeling Language
Unified Victim Identification System database system for critical fatality management Office of Chief Medical Examiner of the City of New York
Unistat statistical data analysis software https://www.unistat.com/
UrQMD Monte Carlo simulation package for Proton+Proton, Proton+nucleus and nucleus+nucleus interactions Goethe University Frankfurt Fortran https://vfs.fias.uni-frankfurt.de/f/b4416cdac5/?raw=1 http://www.th.physik.uni-frankfurt.de/~urqmd
http://urqmd.org
UTOPIA bioinformatics tool
Vaa3D software
Validis software
Verbot chatterbot
Vienna Ab-initio Simulation Package software package for condensed matter physics Fortran https://www.vasp.at
Vienna RNA Package bioinformatics library and set of programs for RNA secondary structure analysis and prediction free software license 2.1.9 Unix
Microsoft Windows
C
Perl
Python
http://www.tbi.univie.ac.at/RNA/
ViEWER software to create virtual displays C++ Microsoft Windows http://webpages.uidaho.edu/~bdyre/viewer.htm
Virtual Cell software platform for modeling and simulation of living organisms, primarily cells MIT license University of Connecticut Health Center Java Microsoft Windows http://vcell.org/webstart/VCell_Tutorials/VCell_Quickstart_6.pdf http://vcell.org Systems Biology Markup Language Systems Biology Markup Language
Nearly Raw Raster Data
VISQ software, from 1993 http://www.modelciencias.furg.br/bin/ferramentas/semi/visq.php
Vnmr software for controlling nuclear magnetic resonance spectrometers proprietary license Varian, Inc. Solaris http://www.varianinc.com/cgi-bin/nav?products/nmr/software/vnmrj&cid=KMPLINPJFM
Voxel-Man software for the creation and visualization of three-dimensional digital models of the human body University Medical Center Hamburg-Eppendorf
VXL collection of open source C++ libraries C++ http://vxl.sourceforge.net
WAsP software for wind resource assessment Technical University of Denmark http://www.wasp.dk/
WaveLab collection of Matlab functions used to implement algorithms related to wavelet analysis http://www-stat.stanford.edu/~wavelab
WEAP decision support system software http://www.weap21.org/
Webtag bioinformatics software
WeBWorK software Artistic License University of Rochester Perl http://webwork.maa.org/
WHAT IF software software for Linux Fortran Linux http://swift.cmbi.ru.nl/whatif Protein Data Bank
WhiskerControl research control system University of Cambridge C++ Windows NT
Windows 2000
Windows XP
Windows Vista
Windows 7
Windows 8
http://www.whiskercontrol.com
WIEN2k software for quantum mechanical calculations on periodic solids TU Wien Fortran 90 http://susi.theochem.tuwien.ac.at/
WIMATS software to transcribe mathematical and scientific text input into braille script for braille presses Webel Mediatronics Limited http://www.webelmediatronics.in/brlads/wimats.htm
WindSim wind farm design tool http://www.windsim.com/products.aspx
WinGX for solving, refining and analysing single crystal X-ray diffraction data for small molecules Windows 2000
Windows XP
Windows Vista
Windows 7
Windows 8
http://www.chem.gla.ac.uk/~louis/software/wingx/
Winplot plotting utility software C++ Microsoft Windows http://math.exeter.edu/rparris/winplot.html
WinStars planetarium, ephemeris and solar system simulator C++ Microsoft Windows
Android
iOS
Linux
macOS
http://www.winstars.net/english/index.html
WMS hydrology software Aquaveo Windows 7
Windows 8
Windows 8.1
Windows 10
http://www.aquaveo.com/wms
http://aquaveo.com/wms
ESRI Arc/Info ASCII Grid
Shapefile
Drawing Interchange Format
AutoCAD Drawing
Tagged Image File Format
JPEG File Interchange Format
WordStat content analysis and text mining add-on module of QDA Miner QDA Miner http://provalisresearch.com/fr/produits/wordstat/
http://www.provalisresearch.com/
WORHP software for Unix-like operating system European Space Agency Unix-like operating system http://www.worhp.de
WorldWide Telescope software for Microsoft Windows, from 2008 MIT license Microsoft C# Microsoft Windows http://worldwidetelescope.org
WUHU weather data uploading software Teechart Microsoft Windows https://wuhusoftware.azurewebsites.net/
WXP Science software http://wxp.unisys.com/
X-12-ARIMA software package for seasonal adjustment public domain United States Census Bureau http://www.census.gov/srd/www/x12a/
xaitment German company http://www.xaitment.com/
XEphem planetarium software Unix-like operating system http://www.clearskyinstitute.com/xephem/ http://www.clearskyinstitute.com/xephem/
XLfit Microsoft Excel-based plug-in which performs regression, curve fitting and statistical analysis Microsoft Excel http://www.excelcurvefitting.com/
Xrate bioinformatics software http://biowiki.org/XRATE Xrate format Xrate format
XSight discontinuted software for qualitative data analysis proprietary license QSR International http://www.qsrinternational.com/products_xsight.aspx/
Yasara computer program for molecular visualising, modelling, and dynamics OpenBabel C Microsoft Windows
Linux
macOS
Android
http://www.yasara.org Protein Data Bank
ZOOMQ3D software http://www.oomodels.info/pmwiki/pmwiki.php/Main/OOModelsHome

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