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Bioclipse

Cheminformatics/Bioinformatics

Bioclipse Description
The Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). It gained scripting functionality in 2009.
Like any RCP application, Bioclipse uses a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. Via its plugins, Bioclipse provides functionality for chemo- and bioinformatics, and extension points that easily can be extended by other, possibly proprietary, plugins to provide additional functionality.
The first stable release of Bioclipse includes a Chemistry Development Kit (CDK) plugin to provide a chemoinformatic backend, a Jmol plugin for 3D-visualization of molecules, and a BioJava plugin for sequence analysis. Recently, the R platform, using StatET, and OpenTox were added.
Bioclipse is developed as a collaboration between the Proteochemometric Group, Dept. of Pharmaceutical Biosciences, Uppsala University, Sweden, the Christoph Steinbeck Group at the European Bioinformatics Institute, and the Analytical Chemistry Department at Leiden University, but also includes extensions developed at other academic institutes, including the Karolinska Institutet and Maastricht University. The development is backed up by the International Bioclipse Association.
A list below shows Bioclipse alternatives which were either selected by us or voted for by users. You can filter this list by tags and platforms

Bioclipse Alternatives

  • UCSF Chimera by Resource for Biocomputing, Visualization, and Informatics (RBVI), UCSF

    UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies,...

    Latest version of UCSF Chimera is 1.11.2 and it was released on 2016-12-02.

    Tags: Bioinformatics Software, Freeware, Molecular Modelling Software, Science Software
  • TreeFinder by Gangolf Jobb

    Treefinder is a computer program for the likelihood-based reconstruction of phylogenetic trees from molecular sequences. It was written by Gangolf Jobb, a former researcher at the University of...

    Latest version of TreeFinder is march2011 and it was released on 2011-03-01.

    Tags: Computational Phylogenetics, Bioinformatics Software, Science Software, Molecular Biology, Genetics
  • TCoffee by Cédric Notredame, Centro de Regulacio Genomica (CRG) - Barcelona

    T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to...

    Latest version of T-Coffee is 11.00.8cbe486 and it was released on 2014-08-13.

    Tags: Bioinformatics Software, Computational Phylogenetics
  • SPAdes by St. Petersburg State University, Russia,St. Petersburg Academic University, Russia,University of California, San Diego, USA

    SPAdes (St. Petersburg genome assembler) is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. However, it might not be suitable for large genomes...

    Latest version of SPAdes is 3.10.1 and it was released on March 1st, 2017.

    Tags: Bioinformatics Algorithms, Bioinformatics Software, Dna Sequencing, Metagenomics Software
  • SEQUEST

    SEQUEST is a tandem mass spectrometry data analysis program used for protein identification. Sequest identifies collections of tandem mass spectra to peptide sequences that have been generated from...

    Tags: Proteomics, Bioinformatics Software, Mass Spectrometry Software
  • by Bennett N.F., Ganesan N Georgetown University

    Sequerome is a web-based Sequence profiling tool for integrating the results of a BLAST sequence-alignment report with external research tools and servers that perform advanced sequence...

    Tags: Bioinformatics Software, Freeware
  • RasMol by Herbert J. Bernstein

    RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data...

    Latest version of RasMol is 2.7.5.1 and it was released on 2009-07-17.

    Tags: Bioinformatics Software, Molecular Modelling Software, Free Science Software, Free Software Programmed In C, Free Educational Software
  • PICRUSt by Morgan Langille,Jesse Zaneveld,Daniel McDonald,Greg Caporaso,Gavin Douglas

    PICRUSt is a bioinformatics software package. The name is an abbreviation for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. The tool serves in the field of...

    Tags: Metagenomics, Bioinformatics Software, Environmental Microbiology
  • Phyre2 by {{Plainlist| * Lawrence Kelley * Bob Maccallum * Benjamin Jefferys * Alex Herbert * Riccardo Bennett-Lovsey *Michael Sternberg}}

    Phyre and Phyre2 (Protein Homology/AnalogY Recognition Engine; pronounced as 'fire') are web-based services for protein structure prediction that are free for non-commercial use. Phyre is among the...

    Latest version of Phyre2 is 2.0 and it was released on 2011-02-23.

    Tags: Bioinformatics Software, Computational Science
  • PHYLogeny Inference Package by University of Washington

    PHYLogeny Inference Package (PHYLIP) is a free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies). It consists of 35 portable programs, i.e., the source...

    Latest version of PHYLogeny Inference Package is 3.696 and it was released on 2014-11-02.

    Tags: Computational Phylogenetics, Bioinformatics Software
  • OpenChrom by Philip Wenig, Alexander Kerner, Lorenz Gerber, Matthias Mailänder, ...

    OpenChrom is an open source software for the analysis and visualization of mass spectrometric and chromatographic data. Its focus is to handle native data files from several mass spectrometry...

    Latest version of OpenChrom is 1.2.0 and it was released on 2017-08-25.

    Tags: Bioinformatics Software, Mass Spectrometry Software, Chemistry Software For Linux, Science Software For Macos, Science Software For Windows, Chromatography Software, Eclipse Software
  • OLIGO Primer Analysis Software by Molecular Biology Insights, Inc.

    OLIGO Primer Analysis Software was the first publicly available software for DNA primer design. The first papers describing this software were published in 1989 and 1990, and consecutive upgrades in...

    Latest version of OLIGO Primer Analysis Software is 7.54 and it was released on March 23, 2011.

    Tags: Bioinformatics Software
  • MUltiple Sequence Comparison by LogExpectation by drive5

    MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain. The method was...

    Latest version of MUltiple Sequence Comparison by Log-Expectation is 3.8.31 and it was released on 2016-08-18.

    Tags: Bioinformatics Software, Computational Phylogenetics
  • Modeller by University of California, San Francisco,Accelrys

    Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). It implements a method...

    Latest version of Modeller is 9.19 and it was released on 2017-07-25.

    Tags: Molecular Modelling Software, Bioinformatics Software, Computational Biology
  • MEGAN by Daniel Huson et al.

    MEGAN ("MEtaGenome ANalyzer") is a computer program that allows optimized analysis of large metagenomic datasets. Metagenomics is the analysis of the genomic sequences from a usually uncultured...

    Latest version of MEGAN is 6.4 and it was released on 2016.

    Tags: Metagenomics Software, Bioinformatics Software, Computational Phylogenetics, Genetics, Molecular Biology
  • Molecular Evolutionary Genetics Analysis by Pennsylvania State University

    Molecular Evolutionary Genetics Analysis (MEGA) is computer software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees. It includes many...

    Latest version of Molecular Evolutionary Genetics Analysis is 7.0.26 and it was released on {{Start date and age|2017|05}}.

    Tags: Data Visualization Software, Bioinformatics Software
  • Mascot

    Mascot is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence databases. Mascot is widely used by research facilities around the world. Mascot uses a...

    Latest version of Mascot is 2.6.00 and it was released on {{Start date and age|2016|12|df=yes}}.

    Tags: Proteomics, Bioinformatics Software, Mass Spectrometry Software
  • Jmol by Jmol development team

    Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in...

    Tags: Bioinformatics Software, Chemistry Software For Linux, Free Chemistry Software, Free Software Programmed In Java, Molecular Modelling Software
  • MacVector by MacVector, Inc.

    MacVector is a commercial sequence analysis application for Apple Macintosh computers running Mac OS X. It is intended to be used by molecular biologists to help analyze, design, research and...

    Latest version of MacVector is 15.5.3 and it was released on [wiki=ecb0313c48409e389f36a444b070e0da]10 July 2016[/wiki].

    Tags: Bioinformatics Software, Computational Science
  • Kepler Scientific Workflow System

    Kepler is a free software system for designing, executing, reusing, evolving, archiving, and sharing scientific workflows. Kepler's facilities provide process and data monitoring, provenance...

    Latest version of Kepler Scientific Workflow System is 2.5 and it was released on 2015-10-28.

    Tags: Workflow Technology, Bioinformatics Software
  • ITASSER by Yang Zhang Lab

    I-TASSER (Iterative Threading ASSEmbly Refinement) is a bioinformatics method for predicting three-dimensional structure model of protein molecules from amino acid sequences. It detects structure...

    Tags: Bioinformatics, Bioinformatics Software
  • HHsearch by Johannes Söding

    HHsearch is an open-source software program for protein sequence searching that is part of the free HH-suite software package. HHpred is a free protein function and protein structure prediction...

    Latest version of HHsearch is 2.0.16 and it was released on 2013-02-18.

    Tags: Bioinformatics Software, Computational Science
  • HHsuite by Johannes Söding, Michael Remmert, Andreas Biegert, Andreas Hauser, Markus Meier, Martin Steinegger

    The HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. These...

    Latest version of HH-suite is 2.0.16 and it was released on 2013-02-18.

    Tags: Bioinformatics Software, Computational Science
  • geWorkbench by Columbia University,,First Genetic Trust,National Cancer Institute

    geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a...

    Latest version of geWorkbench is 2.6.0.3 and it was released on 2016-12-21.

    Tags: Bioinformatics Software, Free Software, Cluster Analysis, Systems Biology, Protein Structure, Gene Expression
  • GenMAPP by Alexander Pico, Kristina Hanspers, Nathan Salomonis, Kam Dahlquist, Scott Doniger, Jeff Lawlor, Alex Zambon, Lynn Ferrante, Karen Vranizan, Steven C. Lawlor, Bruce Conklin

    GenMAPP (Gene Map Annotator and Pathway Profiler) is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in the context of pathways (metabolic,...

    Tags: Bioinformatics Software, Free Science Software, Systems Biology, Windowsonly Free Software
  • GENESIS

    GENESIS (The GEneral NEural SImulation System) is a simulation environment for constructing realistic models of neurobiological systems at many levels of scale including: sub-cellular processes,...

    Latest version of GENESIS is 2.4 and it was released on {{Start date and age|2014|11}}.

    Tags: 1988 Software, Bioinformatics Software, Artificial Intelligence, Software Using The Gpl License
  • GeneMark by Georgia Institute of Technology

    GeneMark is a generic name for a family of ab initio gene prediction programs developed at the Georgia Institute of Technology in Atlanta. Developed in 1993, original GeneMark was used in 1995 as a...

    Tags: Metagenomics Software, Mathematical And Theoretical Biology, Genomics, Bioinformatics Software
  • GeneNetwork by GeneNetwork Development Team, University of Tennessee

    GeneNetwork is a combined database and open source bioinformatics data analysis software resource for systems genetics. This resource is used to study gene regulatory networks that link DNA sequence...

    Latest version of GeneNetwork is 2.0 and it was released on 2017-06-02.

    Tags: Biological Databases, Systems Biology, Bioinformatics Software, Software Using The Gnu Agpl License
  • Galaxy

    Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not...

    Latest version of Galaxy is 17.01 and it was released on 2017-02-23.

    Tags: Bioinformatics Software, Free Software Projects, Workflow Software
  • FastPCR

    FastPCR is an integrated tool for PCR primers or probes design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat...

    Tags: Bioinformatics, Bioinformatics Software, Polymerase Chain Reaction
  • DAVID Bioinformatics Resources by Laboratory of Immunopathogenesis and Bioinformatics

    DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online url=://david.abcc.ncifcrf.gov The DAVID Bioinformatics Resources consists of the DAVID Knowledgebase and...

    Latest version of DAVID Bioinformatics Resources is 6.7 and it was released on 2010-01-27.

    Tags: Biological Databases, Bioinformatics Software, Laboratory Software, Systems Biology
  • CSBLAST by Angermueller C, Biegert A, and Soeding J

    CS-BLAST (Context-Specific BLAST) is a tool that searches a protein sequence that extends BLAST (Basic Local Alignment Search Tool), (Basic Local Alignment Search Tool) using context-specific...

    Latest version of CS-BLAST is 2.2.3 and it was released on 2013-12-07.

    Tags: Bioinformatics Software, Computational Science
  • cTAKES by Apache Software Foundation

    Apache cTAKES: clinical Text Analysis and Knowledge Extraction System is an open-source natural language processing system for information extraction from electronic health record clinical...

    Tags: Apache Software Foundation Projects, Electronic Health Record Software, Natural Language Processing Software, Free Healthcare Software, Bioinformatics Software
  • Coot by Paul Emsley,Kevin D. Cowtan

    The program Coot (Crystallographic Object-Oriented Toolkit) is used to display and manipulate atomic models of macromolecules, typically of proteins or nucleic acids, using 3D computer graphics. It...

    Latest version of Coot is 0.8.7 and it was released on 2016-11-08.

    Tags: Crystallography Software, Molecular Modelling Software, Bioinformatics Software, Free Science Software, Free Chemistry Software, Science Software That Uses Gtk, Science Software For Linux
  • Chemistry Development Kit by The CDK Project

    The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. It is available for Windows, Linux, Unix, and macOS. It...

    Tags: Bioinformatics Software, Chemistry Software For Linux, Computational Chemistry Software, Free Chemistry Software, Free Software Programmed In Java
  • Biopython

    The Biopython Project is an open-source collection of non-commercial Python tools for computational biology and bioinformatics, created by an international association of developers. It contains...

    Latest version of Biopython is 1.70 and it was released on 2017-07-11.

    Tags: Articles With Example Python Code, Bioinformatics Software, Computational Science, Python Scientific Libraries
  • BioPerl

    BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome...

    Latest version of BioPerl is 1.6.924 and it was released on 2014-07-10.

    Tags: Bioinformatics Software, Perl Software, Free Bioinformatics Software
  • BioJava

    BioJava is an open-source software project dedicated to provide Java tools to process biological data. BioJava is a set of library functions written in the programming language Java for manipulating...

    Latest version of BioJava is 4.2.1 and it was released on 2016-01-15.

    Tags: Bioinformatics Software, Java Platform Software
  • Bioconductor

    Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology. Bioconductor is...

    Latest version of Bioconductor is 3.5 and it was released on 2017-04-25.

    Tags: Bioinformatics Software, Free Bioinformatics Software, Free Science Software, Free R Software, Science Software For Macos, Science Software For Windows, Science Software For Linux
  • BioBIKE

    BioBike(nee. BioLingua ) is a cloud-based, through-the-web programmable (Paas) symbolic biocomputing and bioinformatics platform that aims to make computational biology, and especially intelligent...

    Tags: Bioinformatics Software, Free Software Projects, Cloud Computing, Cloud Platforms
  • BioloMICS by BioAware SA NV

    BioloMICS is a bioinformatics software application developed by the company BioAware SA NV. It is tool allowing specialized and scientific biological databases to be created to fit the specific...

    Tags: Bioinformatics Software, Biological Databases
  • BALL project by BALL project team

    BALL (pronounced "ball") is computer software consisting of the versatile C++ class framework Biochemical Algorithms Library (BALL), a set of algorithms and data structures for molecular modelling...

    Latest version of BALL project is 1.4.2 and it was released on 2013-01-28.

    Tags: C Libraries, Computational Chemistry Software, Molecular Modelling Software, Bioinformatics Software, Free Bioinformatics Software, Chemistry Software For Linux, Science Software That Uses Qt, Articles With Example C Code
  • ArrayTrack by U.S. Food and Drug Administration

    ArrayTrack is a multi-purpose bioinformatics tool primarily used for microarray data management, analysis, and interpretation. ArrayTrack was developed to support in-house filter array research for...

    Latest version of ArrayTrack is 3.5.0 and it was released on 2010-03-03.

    Tags: Bioinformatics Software, Microarrays
  • BAliPhy by Benjamin Redelings

    BAli-Phy is a free software program for simultaneously estimating a multiple sequence alignment and its phylogenetic tree. BAli-Phy achieves high accuracy in alignment estimation by using...

    Latest version of BAli-Phy is 2.3.8 and it was released on {{release date and age|16|1|30|df=yes}}.

    Tags: Bioinformatics Software, Computational Phylogenetics
  • Anduril by University of Helsinki

    Anduril is an open source component-based workflow framework for scientific data analysis developed at the Systems Biology Laboratory, University of Helsinki. Anduril is designed to enable...

    Latest version of Anduril is 1.2.23 and it was released on 2014-06-24.

    Tags: Workflow Technology, Bioinformatics Software
  • Pipeline Pilot by Accelrys

    Pipeline Pilot is the authoring tool for the Accelrys Enterprise Platform. It is a scientific visual and dataflow programming language, used in various scientific domains, such as cheminformatics...

    Latest version of Pipeline Pilot is 8.5 CU3 and it was released on {{Start date|2012|05||df=yes/no}}.

    Tags: Science Software, Enterprise Application Integration, Extract Transform Load Tools, Bioinformatics Software, Computational Chemistry Software, Computer Vision Software, Data Analysis Software, Data Mining And Machine Learning Software, Data Visualization Software, Laboratory Software, Mass Spectrometry Software, Natural Language Processing Software, Numerical Software, Plotting Software, Proprietary Software, Visual Programming Languages, Articles Created Via The Article Wizard
  • XRATE by Ian Holmes (UC Berkeley)

    XRATE is a program for prototyping phylogenetic hidden Markov models and stochastic context-free grammars. It is used to discover patterns of evolutionary conservation in sequence alignments. The...

    Tags: Bioinformatics Software
  • WHAT IF by University of Groningen;,EMBL,Heidelberg;,CMBI,Radboud University Nijmegen;,Radboud University Nijmegen Medical Centre (Radboudumc),WHAT IF Foundation

    WHAT IF is a computer program used in a wide variety of computational (in silico) macromolecular structure research fields. The software provides a flexible environment to display, manipulate, and...

    Latest version of WHAT IF is 6.0 and it was released on {{Start date and age|2016|df=yes}}.

    Tags: Molecular Modelling Software, Bioinformatics Software, Protein Structure
  • ViennaRNA Package by Institut für theoretische Chemie, Währingerstr

    The ViennaRNA Package is a set of standalone programs and libraries used for prediction and analysis of RNA secondary structures. The source code for the package is distributed freely and compiled...

    Latest version of ViennaRNA Package is v2.3.3 and it was released on 2017-01-24.

    Tags: Bioinformatics Software, Bioinformatics Algorithms, Computational Biology
  • Vector NTI by Life Technologies

    Vector NTI is a commercial bioinformatics software package used by many life scientists to work, among other things, with nucleic acids and proteins in silico .]It]allows researchers to, for...

    Latest version of Vector NTI is Vector NTI Express v1.1.1 (Mac & Windows); Vector NTI Advance v11.5.2 (Windows & Mac w/PC Emulation) and it was released on 2012-09-20.

    Tags: Bioinformatics Software
  • TPP by Institute for Systems Biology

    The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle...

    Latest version of TPP is 5.0.0 and it was released on 2016-10-11.

    Tags: Free Science Software, Bioinformatics Software, Mass Spectrometry Software, Proteomics, Health Sciences
  • taveRNA by Simon Fraser University

    taveRNA is a software suite for RNA/DNA secondary structure. It is developed in the laboratories for computational biology of the School of Computing Science at the Simon Fraser University. The...

    Tags: Bioinformatics Software, Simon Fraser University
  • TimeTree

    TimeTree is a free public database developed by S. Blair Hedges and Sudhir Kumar, now at Temple University, for presenting times of divergence in the tree of life. The basic concept has been to...

    Tags: Bioinformatics Software
  • Staden Package by James Bonfield, et al.

    The Staden Package is computer software, a set of tools for DNA sequence assembly, editing, and sequence analysis. It is open-source software, released under a BSD 3-clause...

    Latest version of Staden Package is 2.0.0b9 and it was released on 2012-01-24.

    Tags: Bioinformatics Software, Computational Science
  • Sirius by San Diego Supercomputer Center

    Sirius is a molecular modelling and analysis system developed at San Diego Supercomputer Center. Sirius is designed to support advanced user requirements that go beyond simple display of small...

    Latest version of Sirius is 1.2 and it was released on 2008-11-18.

    Tags: Molecular Modelling Software, Bioinformatics Software
  • ShelXle by Christian B. Hübschle

    The program ShelXle is a graphical user interface for the structure refinement program SHELXL. ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res...

    Latest version of ShelXle is 1.0.825 and it was released on 2017-01-28.

    Tags: Crystallography Software, Molecular Modelling Software, Bioinformatics Software, Free Science Software
  • SeqCorator by NoeGen Inc.

    SeqCorator is a bioinformatics software which can run in multiple operating systems (Windows, Mac OS, Unix/Linux) with the same...

    Latest version of SeqCorator is 2.01 and it was released on 2009.

    Tags: Bioinformatics Software
  • Scigress by Fujitsu Limited

    Scigress, stylized SCiGRESS, is a software suite for molecular modelling, computational chemistry, drug design, and materials science, a successor to Computer Aided Chemistry (CAChe)...

    Latest version of Scigress is 2.7(3.2) and it was released on {{Start date and age|2016|05}}.

    Tags: Molecular Modelling Software, Computational Chemistry, Molecular Modelling, Bioinformatics Software, Physics Software, Computational Chemistry Software
  • QuteMol by ISTI,CNR

    QuteMol is an open source, interactive, molecular visualization system. QuteMol utilizes the current capabilities of modern GPUs through OpenGL shaders to offer an array of innovative visual...

    Latest version of QuteMol is 0.4.1 and it was released on 2007-06-06.

    Tags: Molecular Modelling Software, Free Science Software, Chemistry Software For Linux, Free 3d Graphics Software, Free Software Programmed In C, Bioinformatics Software, Software That Uses Wxwidgets
  • ProteoWizard

    ProteoWizard is a set of open-source, cross-platform tools and libraries for proteomics data analyses. It provides a framework for unified mass spectrometry data file access and performs standard...

    Tags: Free Science Software, Bioinformatics Software, Mass Spectrometry Software, Proteomics, Software Using The Apache License
  • PrimerPlex by PREMIER Biosoft

    PrimerPlex designs oligos for standard multiplex PCR assays and for bead-based suspension array systems such as BioPlex-200 and Luminex 100/200 based on xMAP technology. The assays are used for...

    Tags: Bioinformatics Software
  • Primer Premier by Premier Biosoft

    Primer Premier software combines design of primers for various PCR applications under one common platform. The software supports design of degenerate primers on alignments for amplifying related set...

    Tags: Bioinformatics Software
  • Phyloscan by Wadsworth Center, New York State Department of Health

    Phyloscan is a web service for DNA sequence analysis that is free and open to all users (without login requirement). For locating matches to a user-specified sequence motif for a regulatory binding...

    Latest version of Phyloscan is 2.2 and it was released on 2010-01-28.

    Tags: Bioinformatics, Bioinformatics Software, Computational Science
  • Phylogenetic Analysis Using Parsimony and other methods

    PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees (phylogenies), written by David L. Swofford. Originally, as...

    Tags: Computational Phylogenetics, Bioinformatics Software
  • NoePrimer by NoeGen Inc.

    NoePrimer is a bioinformatics software which can run in multiple operating systems (windows, Mac OS, Unix/Linux) with the same...

    Latest version of NoePrimer is 2.01 and it was released on 2009.

    Tags: Bioinformatics Software
  • Newbler by 454 Life Sciences

    Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life...

    Latest version of Newbler is v2.7 and it was released on 2012-02-28.

    Tags: Bioinformatics Software, Computational Science
  • Metascape Bioinformatics Resources by Sanford Burnham, UCSD, GNF

    Metascape is a free gene annotation and analysis resource that helps biologists make sense of one or multiple gene lists. Metascape provides automated meta-analysis tools to understand either common...

    Latest version of Metascape Bioinformatics Resources is 3.0 and it was released on 2016-11-02.

    Tags: Biological Databases, Bioinformatics Software, Laboratory Software, Systems Biology
  • Mesquite A modular system for evolutionary analysis

    Mesquite is a software package primarily designed for phylogenetic analyses. It was developed as a successor to MacClade, when the authors recognized that implementing a modular architecture in...

    Latest version of Mesquite: A modular system for evolutionary analysis is 3.2 and it was released on 2017-01-01.

    Tags: Computational Phylogenetics, Bioinformatics Software, Phylogenetics
  • Mega2 by Daniel E. Weeks, Robert V. Baron, Justin R. Stickel.

    Mega2 (short for manipulation environment for genetic analysis) allows the applied statistical geneticist to convert one's data from several input formats to a large number output formats suitable...

    Latest version of Mega2 is 4.9.2 and it was released on 2017-06-13.

    Tags: Bioinformatics Software, Free Bioinformatics Software
  • MAVID by Nicolas Bray (UC Berkeley), Lior Pachter (UC Berkeley)

    MAVID is a multiple sequence alignment program suitable for the alignment of large numbers of DNA sequences. The sequences can be small mitochondrial genomes or large genomic regions up to megabases...

    Tags: Bioinformatics Software, Computational Phylogenetics
  • LabKey Server by LabKey

    LabKey Server is free, open source software available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure data repository that allows web-based...

    Latest version of LabKey Server is 17.2 and it was released on 2017-07-14.

    Tags: Bioinformatics Software, Free Bioinformatics Software, Free Science Software, Mass Spectrometry Software, Proteomics, Science Software For Windows, Science Software For Linux, Science Software For Macos
  • Jalview by Andrew Waterhouse, James Procter, David Martin and Geoffrey Barton at the University of Dundee.,Original version by Michele Clamp, James Cuff, Stephen Searle, Geoffrey Barton.

    Jalview is a piece of bioinformatics software that is used to look at and edit multiple sequence alignments. It is written in the Java programming language. The programme was originally written by...

    Latest version of Jalview is 2.10.1 and it was released on 2016-11-29.

    Tags: Bioinformatics Software, Computational Phylogenetics
  • Integrated Genome Browser

    Integrated Genome Browser (IGB) (pronounced Ig-Bee) is an open source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence...

    Tags: Bioinformatics Software, Free Bioinformatics Software
  • IMOD by David Mastronarde et al. at the Boulder Laboratory for 3-D Electron Microscopy of Cells

    IMOD is an open-source, cross-platform suite of modeling, display and image processing programs used for 3D reconstruction and modeling of microscopy images with a special emphasis on electron...

    Latest version of IMOD is 4.3.7 and it was released on February 23, 2012.

    Tags: Bioinformatics Software, Science Software, Freeware
  • HyPhy by Sergei L Kosakovsky Pond, Art FY Poon, Steven Weaver, N. Lance Hepler, Martin Smith.

    HYPHY is a free multiplatform (Mac, Windows and UNIX) Computational phylogenetics software package intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to...

    Latest version of HyPhy is June, 2012 and it was released on 2012-06-21.

    Tags: Computational Phylogenetics, Bioinformatics Software
  • GESS by NCSS, LLC

    GESS is a computer program for analyzing gene expression data obtained from microarrays. NCSS LLC is the name of the company that produces GESS. NCSS LLC also produces PASS (Power Analysis and...

    Latest version of GESS is GESS 2006 and it was released on May, 2006.

    Tags: Bioinformatics Software, Microarrays
  • GENtle by Magnus Manske

    GENtle is a free software under GPL...

    Latest version of GENtle is 1.9.0 and it was released on 2006-04-07.

    Tags: Bioinformatics Software, Free Science Software, Science Software For Linux, Software That Uses Wxwidgets
  • GenomeSpace by Broad Institute

    GenomeSpace is an environment for genomics software tools and applications. It helps users manage their analysis workflows involving multiple diverse tools, including web applications and desktop...

    Latest version of GenomeSpace is beta 5.0 and it was released on {{Start date and age|2012|04}}.

    Tags: Bioinformatics Software, Free Bioinformatics Software
  • GenGIS by Donovan Parks, Mike Porter, Timothy Mankowski, Suwen Wang, Sylvia Churcher, Alex Keddy, Christian Blouin, Jacqueline Whalley, Stephen Brooks, Rob Beiko

    GenGIS merges geographic, ecological and phylogenetic biodiversity data in a single interactive visualization and analysis environment. A key feature of GenGIS is the testing of geographic axes that...

    Latest version of GenGIS is 2.4.1 and it was released on 2015.

    Tags: Bioinformatics Software, Biogeography, Genetics, Molecular Biology
  • GenePattern by Broad Institute

    GenePattern is a freely available computational biology open-source software package developed at the Broad Institute of MIT and Harvard for the analysis of genomic data. Designed to enable...

    Latest version of GenePattern is 3.9.8 and it was released on June 2016.

    Tags: Bioinformatics Software, Dna Sequencing, Gene Expression
  • Gene Designer by DNA2.0

    Gene Designer is a computer software package for bioinformatics. It is used by molecular biologists from academia, government, and the pharmaceutical, chemical, agricultural, and biotechnology...

    Latest version of Gene Designer is 2.01.191 and it was released on 2015-10-09.

    Tags: Bioinformatics, Bioinformatics Software
  • Foldit by University of Washington, Center for Game Science, Department of Biochemistry

    Foldit is an online puzzle video game about protein folding. It is part of an experimental research project developed by the University of Washington, Center for Game Science, in collaboration with...

    Tags: 2008 Video Games, Linux Games, Macos Games, Windows Games, Puzzle Video Games, Humanbased Computation Games, Luascripted Video Games, Bioinformatics Software, Computational Biology, Molecular Biology, Protein Folding, Protein Structure, Gamification
  • FlyExpress

    FlyExpress is a free database that collects the expression patterns of Drosophila melanogaster in embryogenesis via a series of images submitted from BDGP, Fly-FISH and publications from other...

    Tags: Insect Developmental Biology, Model Organism Databases, Bioinformatics Software
  • FASTA by Pearson W.R.

    FASTA is a DNA and protein sequence alignment software package first described (as FASTP) by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in...

    Tags: Computational Phylogenetics, Bioinformatics Software
  • esyN

    esyN (Easy Networks) is an open source bioinformatics web-tool for visualizing, building and analysing molecular interaction networks. esyN is based on cytoscape.js and its aim is to make it easy...

    Latest version of esyN (Easy Networks) is 2.1 and it was released on 2016-01-17.

    Tags: Bioinformatics Software, Proteomics, Metabolomic Databases, Free Software
  • eMovie by Israel Structural Proteomics Center

    eMovie is a plug-in for PyMOL that makes the creation of molecular movies both easy and intuitive via a breakthrough storyboard interface, similar in nature to what is used in the creation of...

    Tags: Molecular Modelling Software, Data Visualization Software, Bioinformatics Software
  • DNADynamo by BlueTractorSoftware Ltd

    DNADynamo is a commercial DNA sequence analysis software package produced by Blue Tractor Software Ltd that runs on Microsoft Windows, Mac OS X and Linux It is used by molecular biologists to...

    Tags: Bioinformatics Software, Computational Science
  • DECIPHER by Erik Wright

    Decipher, stylized as DECIPHER, is a software toolset that can be used to decipher and manage biological sequences efficiently using the programming language R. Some functions of the program are...

    Latest version of DECIPHER is 2.2.0 and it was released on {{Start date and age|2016}}.

    Tags: Bioinformatics Software, Computational Phylogenetics
  • Cytoscape

    Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features...

    Latest version of Cytoscape is 3.5.1 and it was released on 2017-04-26.

    Tags: Bioinformatics Software, Systems Biology, Mathematical And Theoretical Biology, Graph Drawing Software, Crossplatform Software, Java Platform Software
  • CLUSTAL by {{Plainlist| * Des Higgins * Fabian Sievers * David Dineen * Andreas Wilm (all at the Conway Institute, UCD)}}

    Clustal is a series of widely used computer programs used in Bioinformatics for multiple sequence...

    Latest version of CLUSTAL is 1.2.2 and it was released on 2016-07-01.

    Tags: Bioinformatics Software, Computational Phylogenetics
  • CheShift2

    CheShift-2 (pronounced /tʃeʃɪft/) is an application created to compute 13Cα and 13Cβ protein chemical shifts and to validate protein structures. It is based on quantum mechanics computations of 13Cα...

    Latest version of CheShift-2 is 3.0 and it was released on 2013-09-01.

    Tags: Bioinformatics Software
  • Budapest Reference Connectome by Balázs Szalkai, Csaba Kerepesi, Bálint Varga, Vince Grolmusz

    The Budapest Reference Connectome server computes the frequently appearing anatomical brain connections of 418 healthy subjects. It has been prepared from diffusion MRI datasets of the Human...

    Tags: Computational Neuroscience, Neuroscience, Neuroinformatics, Bioinformatics, Bioinformatics Software, Free Bioinformatics Software
  • BLAT by Jim Kent,UCSC

    BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the...

    Tags: Bioinformatics Software, Laboratory Software
  • Biskit by Raik Grünberg, Johan Leckner, and others

    Biskit is an open source software package written in Python. The package facilitates research in Structural bioinformatics and molecular modelling. Biskit falls into two parts: * an Object-oriented...

    Tags: Bioinformatics Software, Molecular Modelling, Physics Software, Computational Chemistry Software, Free Science Software, Free Software Programmed In Python, Molecular Dynamics
  • BioPHP

    BioPHP is a collection of open source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools. BioRuby is released under the GNU GPL...

    Tags: Bioinformatics Software, Free Bioinformatics Software
  • BioRuby

    BioRuby is a collection of Open Source Ruby code, comprising classes for computation molecular biology and bioinformatics. It contains classes for DNA and protein sequence analysis, sequence...

    Latest version of BioRuby is 1.5.0 and it was released on 2015-07-01.

    Tags: Bioinformatics Software, Free Bioinformatics Software
  • BioMart

    BioMart is a community-driven project to provide a single point of access to distributed research data. The BioMart project contributes open source software and data services to the international...

    Tags: Bioinformatics Software, Free Software Projects, Biological Databases, Data Warehousing Products
  • BioNumerics by Applied Maths N.V.

    BioNumerics is a suite of bioinformatics software applications developed by the company Applied Maths...

    Tags: Bioinformatics Software
  • Bioinformatic Harvester by Urban Liebel, Björn Kindler

    The Bioinformatic Harvester was a bioinformatic meta search engine created by the European Molecular Biology Laboratory and subsequently hosted and further developed by KIT Karlsruhe Institute of...

    Latest version of Bioinformatic Harvester is 4 and it was released on 2011-05-24.

    Tags: Bioinformatics Software, Biological Databases, Internet Search Engines, Biology Websites
  • Beacon Designer by Premier Biosoft

    Beacon Designer designs highly specific and efficient primers and probes for real time PCR (polymerase chain reaction) assays. It is compatible to work on Windows as well as on Mac. The software...

    Latest version of Beacon Designer is 7.9 and it was released on [wiki=58c032d8e88b253d5577448141ed2384]17 June 2010[/wiki].

    Tags: Bioinformatics Software
  • Archaeopteryx by Christian M. Zmasek

    Archaeopteryx is an interactive computer software program, written in Java, for viewing, editing, and analyzing phylogenetic trees. This type of program can be used for a variety of analyses of...

    Latest version of Archaeopteryx is 0.972+ beta 9M and it was released on 2012.08.08.

    Tags: Bioinformatics Software, Computational Phylogenetics
  • AMPHORA by Martin Wu, Jonathan Eisen et al.

    AMPHORA ("AutoMated Phylogenomic infeRence Application") is an open-source bioinformatics workflow. AMPHORA2 uses 31 bacterial and 104 archaeal phylogenetic marker genes for inferring phylogenetic...

    Latest version of AMPHORA is 2.0 and it was released on 2013.

    Tags: Metagenomics Software, Bioinformatics Software, Free Bioinformatics Software, Computational Phylogenetics, Free Science Software
  • Abalone by Agile Molecule

    Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model) or in...

    Latest version of Abalone is 1.9.0 and it was released on 2016-05-17.

    Tags: Science Software, Molecular Modelling Software, Molecular Dynamics Software, Monte Carlo Software, Bioinformatics Software, Computational Chemistry Software
  • AMAP by Ariel Schwartz (UC Berkeley), Lior Pachter (UC Berkeley)

    AMAP is a multiple sequence alignment program based on a new approach to multiple alignment called sequence annealing. This approach consists of building up the multiple alignment one match at a...

    Tags: Bioinformatics Software
  • AlleleID by PREMIER Biosoft

    AlleleID designs oligos for strain differentiation and taxa specific assays. This aids in bacterial identification, pathogen detection and species identification. The software is designed to run on...

    Latest version of AlleleID is 7.80 and it was released on 29 June 2013.

    Tags: Bioinformatics Software
  • Stemloc by Ian Holmes (UC Berkeley)

    Stemloc is a program for pairwise RNA structural alignment based on probabilistic models of RNA structure known as Pair stochastic context-free grammars. Stemloc implements constrained versions of...

    Tags: Bioinformatics Software
  • SplitsTree by Daniel Huson and David Bryant

    SplitsTree is a popular program for inferring phylogenetic trees or, more generally, phylogenetic networks from various types of data such as a sequence alignment, a distance matrix or a set of...

    Latest version of SplitsTree is 4.14.4 and it was released on 2008.

    Tags: Bioinformatics Software, Computational Phylogenetics, Genetics, Molecular Biology
  • RAPTOR by Bioinformatics Solutions Inc.

    RAPTOR is protein threading software used for protein structure prediction. It has been replaced by RaptorX, which is much more accurate than...

    Latest version of RAPTOR is 4.2 and it was released on {{Start date and age|2008|11}}.

    Tags: Bioinformatics Software, Molecular Modelling Software
  • NoeClone by NoeGen Inc.

    NoeClone is a bioinformatics software which can run in multiple operating systems (Windows, Mac OS, Unix/Linux) with the same...

    Latest version of NoeClone is 2.01 and it was released on 2009.

    Tags: Bioinformatics Software
  • MAFFT by Kazutaka Katoh

    In bioinformatics, MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences. The software is named after the acronym Multiple Alignment using Fast Fourier Transform...

    Latest version of MAFFT is 7.299 and it was released on 2016-06-28.

    Tags: Bioinformatics Software, Computational Phylogenetics
  • Handel by Ian Holmes (UC Berkeley)

    Handel is a suite of programs for multiple sequence alignment. Since it is based on a model of DNA sequence evolution that explicitly incorporates insertion and deletion events, it effectively...

    Tags: Bioinformatics Software
  • Giant Virus Finder by Csaba Kerepesi

    The Giant Virus Finder is a free bioinformatics software for finding giant viruses in...

    Tags: Metagenomics Software, Bioinformatics Software, Free Bioinformatics Software, Free Science Software
  • GENSCAN by Christopher Burge

    In bioinformatics GENSCAN is a program to identify complete gene structures in genomic DNA. It is a GHMM-based program that can be used to predict the location of genes and their exon-intron...

    Tags: Bioinformatics Software
  • Dendroscope by Daniel Huson et al.

    Dendroscope is an interactive computer software program written in Java for viewing Phylogenetic trees. This program is designed to view trees of all sizes and is very useful for creating figures....

    Latest version of Dendroscope is 3.2.10 and it was released on 2013.

    Tags: Bioinformatics Software, Computational Phylogenetics
  • Apache Taverna by Apache Software Foundation (myGrid for 2.x)

    Apache Taverna is an open source software tool for designing and executing workflows, initially created by the myGrid project under the name Taverna Workbench, now a project under the Apache...

    Latest version of Apache Taverna is 2.5 and it was released on 2014-04-16.

    Tags: Workflow Technology, Bioinformatics Software, School Of Computer Science University Of Manchester, Workflow Software, Apache Software Foundation, Apache Software Foundation Projects, Software Using The Apache License
  • BLAST by Altschul SF,Gish W,Miller W,Myers EW,Lipman DJ,NCBI

    In bioinformatics, BLAST for Basic Local Alignment Search Tool is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides...

    Latest version of BLAST is 2.6.0+ and it was released on 2016-12-07.

    Tags: Bioinformatics Algorithms, Computational Phylogenetics, Bioinformatics Software, Laboratory Software, Publicdomain Software
  • HMMER by Sean Eddy, Travis Wheeler, HMMER development team

    HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence...

    Latest version of HMMER is 3.0 and it was released on 2010-03-28.

    Tags: Bioinformatics Software, Free Science Software, Free Software Programmed In C, Computational Science
  • MorphoBank by The MorphoBank Project

    MorphoBank is a web application for collaborative evolutionary research, specifically phylogenetic systematics or cladistics, on the phenotype. Historically, scientists conducting research on...

    Tags: Web Applications, Bioinformatics Software
  • OpenMS

    OpenMS is an open-source project for data analysis and processing in protein mass spectrometry and is released under the 3-clause BSD licence. It supports most common operating systems including...

    Latest version of OpenMS is 2.1.0 and it was released on 2016-11-22.

    Tags: Free Science Software, Bioinformatics Software, Mass Spectrometry Software, Proteomics, Software Using The Bsd License
  • UGENE by Unipro

    UGENE is computer software for bioinformatics. It works on desktop computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General...

    Latest version of UGENE is 1.27 and it was released on 2017-08-23.

    Tags: Bioinformatics Software, Free Science Software, Free Software Programmed In C, Computational Science
  • Molekel by Swiss National Supercomputing Centre

    Molekel is a free software multiplatform molecular visualization program. It was originally developed at the University of Geneva by Peter F. Flükiger in the 1990s for Silicon Graphics Computers. In...

    Latest version of Molekel is 5.4 and it was released on {{Start date and age|2009|08}}.

    Tags: Chemistry Software For Linux, Free Chemistry Software, Molecular Modelling Software, Science Software That Uses Qt
  • PyMOL by Schrödinger, Inc.

    PyMOL is computer software, a molecular visualization system created by Warren Lyford DeLano. It is user-sponsored, open-source software, released under the Python License. It was commercialized...

    Latest version of PyMOL is 1.8.6.2 and it was released on 2017-06-26.

    Tags: Articles Containing Video Clips, Chemistry Software For Linux, Free Chemistry Software, Molecular Modelling Software, Software That Uses Tk
  • Open Babel by Open Babel development team

    Open Babel is computer software, a chemical expert system mainly used to interconvert chemical file formats. Due to the strong relationship to informatics this program belongs more to the category...

    Latest version of Open Babel is 2.4.0 and it was released on 2016-09-25.

    Tags: Computational Chemistry Software, Free Chemistry Software, Free Software Programmed In C, Chemistry Software For Linux, Software That Uses Wxwidgets
  • Ghemical

    Ghemical is a computational chemistry software package written in C++ and released under the GNU General Public License. The program has graphical user interface based on GTK+2 and supports quantum...

    Tags: Computational Chemistry Software, Free Software Programmed In C, Free Chemistry Software, Free Educational Software, Science Software That Uses Gtk
  • Gabedit by A.R. ALLOUCHE

    Gabedit is a Graphical User Interface to GAMESS (US), Gaussian, MOLCAS, MOLPRO, MPQC, OpenMopac, PC GAMESS, Orca and Q-Chem computational chemistry...

    Latest version of Gabedit is 2.4.8 and it was released on 2014-02-07.

    Tags: Computational Chemistry Software, Scientific Software That Uses Gtk, Free Chemistry Software, Chemistry Software For Linux
  • CP2K

    CP2K is a freely available (GPL) program, written in Fortran 2003, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general...

    Latest version of CP2K is 4.1 and it was released on 2016-10-05.

    Tags: Free Physics Software, Free Software Programmed In Fortran, Density Functional Theory Software, Computational Chemistry Software, Free Chemistry Software, Chemistry Software For Linux
  • Avogadro

    Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible...

    Latest version of Avogadro is Avogadro 1.2 and it was released on 2016-06-15.

    Tags: Free Chemistry Software, Free Software Programmed In C, Molecular Modelling Software, Computational Chemistry Software, Science Software That Uses Qt, Chemistry Software For Linux
  • JChemPaint by The CDK Project

    JChemPaint is computer software, an molecule editor and file viewer for chemical structures using 2D computer graphics. It is free and open-source software, released under a GNU Lesser General...

    Tags: Chemistry Software, Free Chemistry Software, Chemistry Software For Linux, Free Educational Software
  • BKChem by Beda Kosata

    BKChem is a free 2D molecule editor written in Python by Beda Kosata. As such, it is largely platform-independent. It uses Tk via...

    Latest version of BKChem is 0.13.0 and it was released on 2009-02-23.

    Tags: Free Software Programmed In Python, Chemistry Software, Free Chemistry Software, Software That Uses Tk, Chemistry Software For Linux
  • NWChem by Pacific Northwest National Laboratory

    NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality. It was designed to run on high-performance parallel...

    Latest version of NWChem is 6.6 and it was released on October 20, 2015.

    Tags: Computational Chemistry Software, Free Chemistry Software, Chemistry Software For Linux
  • PSI4 by The PSI4 Project

    PSI is an ab initio computational chemistry package originally written by the research group of Henry F. Schaefer, III (University of Georgia). Utilizing PSI, one can perform a calculation on a...

    Latest version of PSI4 is PSI4 1.1 and it was released on 2017-05-19.

    Tags: Computational Chemistry Software, Free Chemistry Software, Chemistry Software For Linux
  • RSSOwl by Benjamin Pasero

    RSSOwl is a news aggregator for RSS and Atom News feeds. It is written in Java, and is built on the Eclipse Rich Client Platform which uses SWT as a widget toolkit to allow it to fit in with the...

    Tags: 2004 Software, Free News Aggregators, Java Platform Software, Macos Internet Software, Windows Internet Software, Solaris Software, Portable Software, Crossplatform Software, News Aggregator Software, Software Using The Eclipse License
  • HSQLDB

    HSQLDB (Hyper SQL Database) is a relational database management system written in Java. It has a JDBC driver and supports a large subset of SQL-92, SQL:2008, and SQL:2011 standards. It offers a...

    Latest version of HSQLDB (HyperSQL DataBase) is 2.4.0 and it was released on 2017-04-09.

    Tags: Free Database Management Systems, Java Platform Software, Sql, Relational Database Management Systems, Rdbms Software For Linux, Software Using The Bsd License
  • Jaikoz by Jthink

    Jaikoz is a Java program used for editing and mass tagging music file tags. Jaikoz generates acoustic fingerprints from music files using the AcoustId service, it can then look up the metadata from...

    Latest version of Jaikoz is 9.0.1 and it was released on 2016-11-05.

    Tags: Online Music Database Clients, Shareware, Java Platform Software, Macos Multimedia Software, Windows Multimedia Software, Multimedia Software For Linux, Tag Editors, Acoustic Fingerprinting, Computerrelated Introductions In 2006
  • OpenNMS by The Order of the Green Polo,The OpenNMS Group

    OpenNMS is a free and open-source enterprise grade network monitoring and network management platform. It is developed and supported by a community of users and developers as well as by the The...

    Latest version of OpenNMS is 20.0.2 and it was released on 2017-08-17.

    Tags: Network Management, System Administration, Computer Network Analysis, Network Performance, Free Network Management Software, Free Software Programmed In Java, Java Platform Software, Software Using The Gnu Agpl License
  • OpenGrok by Sun Microsystems/Oracle Corporation

    OpenGrok is a source code search and cross reference engine. It helps programmers to search, cross-reference and navigate source code trees. It can understand various program file formats and...

    Latest version of OpenGrok is 1.0 and it was released on 2017-04-01.

    Tags: Crossplatform Free Software, Free Version Control Software, Source Code, Java Platform Software, Concurrent Versions System, Subversion, Code Search Engines
  • BioFabric by Institute for Systems Biology

    BioFabric is an open source software application for graph drawing. It presents graphs as a node-link diagram, but unlike other graph drawing tools that depict the nodes using discrete symbols, it...

    Latest version of BioFabric is 1.0.0 and it was released on 27 July 2012.

    Tags: Systems Biology, Graph Drawing Software, Crossplatform Software, Java Platform Software
  • BioTapestry by Institute for Systems Biology

    BioTapestry is an open source software application for modeling and visualizing gene regulatory networks...

    Latest version of BioTapestry is 7.0.0 and it was released on 22 September 2014.

    Tags: Systems Biology, Graph Drawing Software, Crossplatform Software, Java Platform Software
  • Zekr by Mohsen Saboorian et al.

    Zekr (Arabic:ذکر) is an open source Quranic desktop application. It is an open platform Quran study tool for browsing and researching on the Quran. Zekr is a Quran-based project, planned to be a...

    Tags: Quran Software, Free Software Programmed In Java, Unix Software, Windows Textrelated Software, Macos Textrelated Software, Macos Software, Java Platform Software
  • parboiled Library by Mathias Doenitz

    parboiled is an open-source Java library released under an Apache License. It provides support for defining PEG parsers directly in Java source code. parboiled is commonly used as an alternative...

    Latest version of parboiled Library is 1.1.7 and it was released on 2015-02-09.

    Tags: Xml Software, Java, Java Platform Software, Computer Libraries, Free Computer Programming Tools, Parser Generators
  • Makagiga by Konrad Twardowski, Makagiga Team

    Makagiga is a portable application for doing a variety of tasks, such as todo listing, note taking, or RSS reading. Plugins (Add-ons) are used to implement its various...

    Latest version of Makagiga is 5.8.2 and it was released on 2017-04-24.

    Tags: Free Task Management Software, Widget Engines, News Aggregator Software, Free News Aggregators, Java Platform Software, Portable Software, 2005 Software
  • Behaviour Composer by University of Oxford Modelling4All Project

    Behaviour Composer is an open-source web app for creating and running NetLogo agent-based models. Behaviour Composer was developed at the University of Oxford in England by the Modelling4All Project...

    Tags: 2007 Software, Web Applications, Free Web Software, Java Platform Software
  • PathVisio

    PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for...

    Latest version of PathVisio is 3.2.4 and it was released on November 24, 2016.

    Tags: Free Bioinformatics Software, Systems Biology, Data Visualization Software, Mathematical And Theoretical Biology, Crossplatform Software, Java Platform Software
  • JADE

    Java Agent DEvelopment Framework, or JADE, is a software framework for the development of intelligent agent, implemented in Java. JADE system supports coordination between several agents FIPA and...

    Latest version of JADE is 4.4 and it was released on 2015-12-23.

    Tags: Agentbased Software, Java Platform Software, Multiagent Systems
  • JACK Intelligent Agents

    JACK Intelligent Agents is a framework in Java for multi-agent system development. JACK Intelligent Agents was built by Agent Oriented Software Pty. Ltd. (AOS) and is a third generation agent...

    Latest version of JACK Intelligent Agents is 5.6 and it was released on 2015-07-01.

    Tags: Java Platform Software, Agentbased Software, Multiagent Systems
  • SPSS by IBM Corporation

    SPSS Statistics is a software package used for logical batched and non-batched statistical analysis. Long produced by SPSS Inc., it was acquired by IBM in 2009. The current versions (2015) are...

    Latest version of SPSS is 25.0 and it was released on 2017-08-08.

    Tags: Ibm Software, Java Platform Software, Proprietary Commercial Software For Linux, Science Software For Linux, Statistical Programming Languages, Statistical Software
  • Vuze by Azureus Software

    Vuze (previously Azureus) is a BitTorrent client used to transfer files via the BitTorrent protocol. Vuze is written in Java, and uses the Azureus Engine. In addition to downloading data linked to...

    Tags: 2003 Software, Java Platform Software, Macos File Sharing Software, Bittorrent Clients For Linux, Windows File Sharing Software
  • TopBT by The Ohio State University

    TopBT (originally called Top-BT), is a topology-aware BitTorrent client implemented with open-source Vuze code base Version 4.0.0.4. It is developed as a research result from The Ohio State...

    Tags: Free Bittorrent Clients, Free Software Programmed In Java, Bittorrent Clients For Linux, Windows File Sharing Software, Java Platform Software
  • OneSwarm by University of Washington

    OneSwarm is a privacy-preserving P2P client developed at the University of Washington. Although backward compatible with traditional BitTorrent clients, OneSwarm also includes new features designed...

    Tags: Free Bittorrent Clients, Free Software Programmed In Java, Java Platform Software, Bittorrent Clients For Linux, Macos File Sharing Software, Windows File Sharing Software, Anonymous File Sharing Networks
  • JavaPolyjs

    JavaPoly is a library that polyfills native JVM support within any modern web browser. This allows websites to import Java libraries, and call them directly from Javascript, even if the user does...

    Tags: Java, Java Platform Software, Java Specification Requests, Java Virtual Machine, Javascript Libraries, Web Development Software, Rich Internet Application Frameworks, Java Platform
  • Forscene by Forbidden Technologies plc.

    Forscene is an integrated internet video platform, video editing software, covering non linear editing and publishing for broadcast, web and mobile. Designed by Forbidden Technologies plc to allow...

    Latest version of Forscene is Forscene and it was released on 2007-01-25.

    Tags: Film And Video Technology, Java Platform Software, Publishing Software, Video Editing Software, Video Hosting, Web Applications, Web Hosting
  • Remote Component Environment by German Aerospace Center (DLR)

    The remote component environment (RCE) is an integration environment for scientists and engineers to analyze, design, and simulate complex systems (e.g., aircraft, satellites, and space vehicle). It...

    Latest version of Remote Component Environment (RCE) (Was: Reconfigurable Computing Environment) is 5.0.0 and it was released on 2014-05-15.

    Tags: Java Platform Software, Grid Computing Projects, Distributed Computing Architecture, Scientific Simulation Software
  • Jinfonet JReport Suite by Jinfonet Software

    Jinfonet Software Inc provides the JReport product suite, a Java reporting solution that delivers customizable business intelligence. The product, JReport, can be deployed as an embedded reporting...

    Latest version of Jinfonet JReport Suite is 14 Update 2 and it was released on 2017-03-14.

    Tags: Java Platform Software, Reporting Software, Business Intelligence
  • FriendCaller by C2Call GmbH

    FriendCaller is a Video and Voice over Internet protocol developed by C2Call GmbH based in Werl, Germany. Its proprietary Voice-Over-Internet technology was originally created by Michael Knecht and...

    Tags: Android Software, Crossplatform Software, Java Platform Software, Freeware, Ios Software, Instant Messaging Clients For Linux, Macos Instant Messaging Clients, Portable Software, Social Networking Services, Videotelephony, Voip Services, Voip Companies, Voip Software
  • inet Clear Reports

    i-net Clear Reports (formerly known as i-net Crystal-Clear) is a Java-based cross-platform reporting application providing a report designer and a server component to create reports in numerous...

    Latest version of i-net Clear Reports (formerly i-net Crystal-Clear) is 11.0 and it was released on May 16, 2011.

    Tags: Java Platform Software, Net Framework Software, Reporting Software, Business Intelligence
  • Openfire by Ignite Realtime

    Openfire (previously known as Wildfire, and Jive Messenger) is an instant messaging (IM) and groupchat server that uses XMPP server written in Java and licensed under the Apache License...

    Latest version of Openfire is 4.1.3 and it was released on 2017-02-24.

    Tags: Java Platform Software, Instant Messaging Server Software, Free Software Programmed In Java
  • Java Desktop System by Oracle Corporation

    Java Desktop System, briefly known as OpenSolaris Desktop, is a desktop environment developed first by Sun Microsystems and then by Oracle Corporation after the 2010 Oracle acquisition of Sun. Java...

    Tags: Desktop Environments, Java Platform Software, Oracle Corporation, Oracle Software, Sun Microsystems Software
  • CoNTub

    CoNTub is a software project written in Java which runs on Windows, Mac OS X, Linux and Unix Operating systems through any Java-enabled web browser. It is the first implementation of an algorithm...

    Latest version of CoNTub is 2.0 and it was released on {{release date and age |2011|09}}.

    Tags: Molecular Modelling Software, Freeware, Science Software, Java Platform Software
  • FrontBase by FrontBase, Inc.

    FrontBase is a relational database management system written in ANSI C. FrontBase uses the Unicode character...

    Latest version of FrontBase is 8.2.6 and it was released on 2015-12-15.

    Tags: Java Platform Software, Sql, Relational Database Management Systems, Rdbms Software For Linux
  • DocFetcher by DocFetcher project

    DocFetcher is an open source desktop search application that runs on Microsoft Windows, Mac OS X and Linux. It is written in Java and has a Standard Widget Toolkit based graphical user...

    Latest version of DocFetcher is 1.1.19 and it was released on Jan, 10, 2017.

    Tags: Desktop Search Engines, Free Search Engine Software, Crossplatform Software, Java Platform Software, Free Software Programmed In Java
  • XStream Library by Codehaus

    XStream is a Java library to serialize objects to XML (or JSON) and back...

    Latest version of XStream Library is 1.4.10 and it was released on 2017-05-23.

    Tags: Xml Software, Java, Java Platform Software, Computer Libraries, Free Computer Programming Tools
  • JasperReports by Jaspersoft

    JasperReports is an open source Java reporting tool that can write to a variety of targets, such as: screen, a printer, into PDF, HTML, Microsoft Excel, RTF, ODT, Comma-separated values or XML...

    Latest version of JasperReports is 6.4.1 and it was released on 2017-06-28.

    Tags: Java Platform Software, Reporting Software, Free Reporting Software, Free Software Programmed In Java, Business Intelligence
  • OpenProj by Marc O'Brien, Howard Katz, Laurent Chrettieneau

    OpenProj is an open source project management software...

    Latest version of OpenProj is OpenProj 1.4 and it was released on 2008.

    Tags: Free Software Programmed In Java, Free Project Management Software, Java Platform Software
  • TuxGuitar

    TuxGuitar is a free, open source tablature editor, which includes features such as tablature editing, score editing, and import and export of Guitar Pro gp3, gp4, and gp5 files. In addition,...

    Latest version of TuxGuitar is 1.4 and it was released on 2016-12-22.

    Tags: Guitarrelated Software, Java Platform Software, Crossplatform Software, Scorewriters, Free Music Software, Audio Software That Uses Gtk, Scorewriters For Linux
  • ImageMagick by ImageMagick Studio LLC

    ImageMagick is a free and open-source software suite for displaying, converting, and editing raster image and vector image files. It can read and write over 200 image file...

    Latest version of ImageMagick is 7.0.6-1 and it was released on 2017-07-15.

    Tags: 1990 Software, Commandline Software, Free Graphics Software, Free Raster Graphics Editors, Free Software Programmed In C, Graphics Libraries, Graphics Software, Irix Software, Java Platform Software, Screenshot Software
  • CaRMetal by Eric Hakenholz, Patrice Debrabant, Pierre-Marc Mazat, Alain Busser

    CaRMetal is an interactive geometry program which inherited the C.a.R. engine. The software has been created by Eric Hakenholz, in Java. CaRMetal is free, under GNU GPL license. It keeps an amount...

    Latest version of CaRMetal is 3.8.7 and it was released on 2015-05-25.

    Tags: Free Educational Software, Free Interactive Geometry Software, Java Platform Software
  • OpenKM by OpenKM

    OpenKM is a Free/Libre document management system that provides a web interface for managing arbitrary files. OpenKM includes a content repository, Lucene indexing, and jBPM workflow. The OpenKM...

    Latest version of OpenKM is 6.3.0 and it was released on 2014-05-21.

    Tags: Free Content Management Systems, Free Software Programmed In Java, Java Platform Software, Document Management Systems, Free Groupware, Free Business Software
  • OWASP ZAP

    OWASP ZAP (short for Zed Attack Proxy) is an ] web application security scanner. It is intended to be used by both those new to application security as well as professional penetration testers. It...

    Latest version of OWASP ZAP is 2.4.3 and it was released on 2015-12-04.

    Tags: Computer Network Security, Computer Security Software, Crossplatform Free Software, Free Security Software, Injection Exploits, Java Platform Software, Web Security Exploits, Web Development Software
  • VisualAp

    VisualAp is a visual framework for building applications and emulate systems. VisualAp is cross-platform as it is a 100% Java application. This application is able to perform audio processing,...

    Tags: Image Processing Software, Free Audio Software, Java Libraries, Java Platform Software, Free Software Programmed In Java
  • YaCy by YaCy community

    YaCy (pronounced "ya see") is a free distributed search engine, built on principles of peer-to-peer (P2P) networks. Its core is a computer program written in Java distributed on several hundred...

    Latest version of YaCy is 1.92 and it was released on 2016-12-26.

    Tags: Anonymity Networks, Distributed Data Storage, Free Search Engine Software, Free Web Crawlers, Internet Search Engines, Java Platform Software, Crossplatform Software, Software Using The Gpl License, Peertopeer Software
  • ImageJ by Wayne Rasband (retired from NIH)

    ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health. ImageJ was designed with an open architecture that provides extensibility via Java...

    Latest version of ImageJ is 1.51n and it was released on 2017-05-01.

    Tags: Free Science Software, Free Dicom Software, Free Bioimaging Software, Java Libraries, Java Platform Software, Free Software Programmed In Java, Publicdomain Software With Source Code
  • ProjectLibre by Marc O'Brien, Laurent Chrettieneau

    ProjectLibre is an open source, freely available project management software system intended ultimately as a standalone replacement for Microsoft Project. ProjectLibre is written in the Java...

    Latest version of ProjectLibre is 1.7.0 and it was released on 2017-01-16.

    Tags: Free Software Programmed In Java, Free Project Management Software, Java Platform Software
  • Statmetrics by Alex Vinnitschenko

    Statmetrics is a free cross-platform software application providing an interactive environment for computational finance. Statmetrics is an analytical tool which offers several modeling techniques...

    Tags: Financial Markets, Financial Software, Financial Markets Software, Technical Analysis Software, Crossplatform Software, Java Platform Software
  • LimeWire by Lime Wire LLC

    LimeWire was a free peer-to-peer file sharing (P2P) client program that ran on Windows, Mac OS X, Linux, and other operating systems supported by the Java software platform. LimeWire used the...

    Latest version of LimeWire is 5.5.16 and it was released on 2010-10-26.

    Tags: 2000 Software, Java Platform Software, Windows File Sharing Software, Classic Mac Os Software, Macos File Sharing Software, File Sharing Software For Linux, Free File Sharing Software, Free Bittorrent Clients, Free Software Programmed In Java, Crossplatform Software, Software That Bundles Malware, Internet Services Shut Down By A Legal Challenge, Bittorrent Clients For Linux
  • OLAT by in association with the community

    OLAT is an acronym for Online Learning And Training. It is a web application - a so-called Learning Management System that supports any kind of online learning, teaching, and tutoring with few...

    Latest version of OLAT is 7.6 and it was released on September 17, 2012.

    Tags: Free Learning Management Systems, Free Educational Software, Virtual Learning Environments, Java Platform Software, Software Using The Apache License
  • CaR

    C.a.R.- Compass and Ruler (also known as Z.u.L., which stands for the German "Zirkel und Lineal") - is a free and open source interactive geometry app that can do geometrical constructions in...

    Tags: Free Educational Software, Free Interactive Geometry Software, Java Platform Software
  • Traction TeamPage by Traction Software

    Traction TeamPage is a proprietary enterprise 2.0 social software product developed by Traction Software Inc of Providence, Rhode Island. TeamPage is one of the first products in the enterprise...

    Latest version of Traction TeamPage is 6.1 (24) and it was released on 2016-12-10.

    Tags: Content Management Systems, Java Platform Software, Proprietary Wiki Software, Blog Software, Collaboration, Groupware
  • Collaber

    Collaber is a collaboration software built on Eclipse Software RCP. Collaber Features include File sharing, Task management, Shared Calendar, Group Discussion. It contains Tools like Address Book,...

    Latest version of Collaber is 1.2 and it was released on 2009-02-19.

    Tags: Distributed Data Storage, Freeware, Groupware, Java Platform Software, Collaborative Software, Internet Software For Linux, Macos Internet Software, Windows Internet Software, File Hosting For Linux, File Hosting For Macos, File Hosting For Windows
  • Compendium by Compendium Institute

    Compendium is a computer program and social science tool that facilitates the mapping and management of ideas and arguments. The software provides a visual environment that allows people to...

    Tags: Argument Mapping, Collaborative Software, Java Platform Software, Mindmapping Software, Notetaking Software, Free Qda Software, Free Software Programmed In Java, Concept And Mindmapping Software Programmed In Java
  • Collanos Workplace by Collanos Software

    Collanos Workplace is a proprietary teamwork software that ceased development in 2010. Installed on each team member’s computer, it builds a team environment and transparent knowledge store that...

    Latest version of Collanos Workplace is 1.4 and it was released on 2008-12-11.

    Tags: Distributed Data Storage, Freeware, Groupware, Java Platform Software, Collaborative Software, Software Companies Of Ukraine, Internet Software For Linux, Macos Internet Software, Windows Internet Software, File Hosting For Linux, File Hosting For Macos, File Hosting For Windows, Peertopeer Software
  • Sakai Project

    Sakai is a free, community source, educational software platform designed to support teaching, research and collaboration. Systems of this type are also known as Course Management Systems (CMS),...

    Latest version of Sakai Project is 11.4 and it was released on 2017-06-02.

    Tags: Educational Technology Projects, Educational Software, Virtual Learning Environments, Free Learning Management Systems, Learning Management Systems, Free Educational Software, Free Content Management Systems, Java Platform Software, Free Software Projects, 2005 Software
  • LibrePlan by Igalia

    LibrePlan is a free software web application for project management, developed by the Fundación para o Fomento da Calidade Industrial e Desenvolvemento Tecnolóxico de Galicia, dependent of the...

    Latest version of LibrePlan is 1.4.1 and it was released on 2015-04-21.

    Tags: Free Application Software, Project Management, Free Software Programmed In Java, Free Project Management Software, Java Platform Software, Software Using The Gnu Agpl License