Cytoscape Alternatives

Cytoscape is described as 'Open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web' and is an app in the social & communications category. There are more than 10 alternatives to Cytoscape for a variety of platforms, including Windows, Mac, Linux, Web-based and iPad apps. The best Cytoscape alternative is Gephi, which is both free and Open Source. Other great apps like Cytoscape are ikolinks, Tabnetviz, Linkurious and NodeXL.

Cytoscape iconCytoscape
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  • Free • Open Source
  • ...

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of...

More about Cytoscape
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Cytoscape alternatives page was last updated Oct 26, 2023
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  1. Gephi icon

    Gephi

     57 likes
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    Gephi is the leading visualization and exploration software for all kinds of graphs and networks. Gephi is open-source and free.

    48 Gephi alternatives

    License model

    • Free • Open Source

    Application type

    Country of Origin

    • FR flagFrance
    • European Union flagEU

    Platforms

    • Mac
    • Windows
    • Linux
    Gephi screenshot 1

    Properties

    1.  Lightweight

    Features

    1.  Extensible by Plugins/Extensions
    2.  Layout
    3.  Exploration
    4.  Graphs
    5.  Interactive Graph Exploration
    6.  Filtering
    7.  Java based
    8.  Data visualization
    9.  3D Renderer

    Gephi VS Cytoscape

     

    • Gephi is the most popular Windows, Mac & Linux alternative to Cytoscape.

    • Gephi is the most popular Open Source & free alternative to Cytoscape.

    • Gephi is Free and Open SourceCytoscape is also Free and Open Source
    • Gephi is LightweightCytoscape is not according to our users
  2. ikolinks icon

    ikolinks

     1 like
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    Explore a world of curated content, helpful resources, and exciting updates. Sign Up below to discover more about Bio Links Tool. Do everything with one platform.

    License model

    Platforms

    • Online
    ikolinks screenshot 1

    ikolinks Features

    1.  Real time collaboration
    2.  Marketing Automation
    3.  Ad-free
    4.  Website Monitoring
    5.  No Coding Required
    6.  Data analytics
    7.  Real-time analytics
    8.  AI-Powered

    ikolinks VS Cytoscape

     

    • ikolinks is the most popular Web-based alternative to Cytoscape.

    • ikolinks is the most popular commercial alternative to Cytoscape.

    • ikolinks is Paid and ProprietaryCytoscape is Free and Open Source
  4. Tabnetviz icon

    Tabnetviz

     4 likes
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    table-based network visualizer, a command-line tool for producing static network visualizations from a node table and an edge table.

    6 Tabnetviz alternatives

    License model

    • Free • Open Source

    Application type

    Platforms

    • Mac
    • Windows
    • Linux
    • Python
    Network visualization generated by Tabnetviz.

    Tabnetviz Features

    1.  Command line interface
    2.  Plot visualisation
    3.  Graphs
    4.  Data visualization
    5.  Bioinformatics

    Tabnetviz VS Cytoscape

     
  5. Linkurious icon

    Linkurious

     9 likes
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    Linkurious provides a graph visualization and analysis platform used for fraud detection, anti-money laundering, intelligence or cybersecurity. Easy to deploy and highly extensible, Linkurious Enterprise makes it easy to uncover insights hidden in complex connected data.

    License model

    Country of Origin

    • FR flagFrance
    • European Union flagEU

    Platforms

    • Online
    Explore and make sense of graph data through Linkurious Enterprise simple web-based interface.

    Linkurious Features

    1.  Graphs
    2.  Data visualization
    3.  Graph database
    4.  Data analytics
    5.  Fraud detection

    Linkurious VS Cytoscape

     
  6. NodeXL icon

    NodeXL

     6 likes
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    NodeXL is a free, open-source template for Microsoft® Excel® 2007 and 2010 that makes it easy to explore network graphs. With NodeXL, you can enter a network edge list in a worksheet, click a button and see your graph, all in the familiar environment of the Excel...

    12 NodeXL alternatives

    License model

    • Free • Open Source

    Platforms

    • Windows
    • Microsoft Office Excel

    NodeXL Features

    1.  Excel Add-in

    NodeXL VS Cytoscape

     
  7. Wandora.org icon

    Wandora.org

     7 likes
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    Wandora is a general purpose information extraction, management and publishing application based on Topic Maps and Java. Wandora has graphical user interface, layered and merging information model, multiple visualization models, huge collection of information extraction, import...

    License model

    • Free • Open Source

    Platforms

    • Mac
    • Windows
    • Linux
    Wandora.org screenshot 1

    Wandora.org VS Cytoscape

     
  9. Graphia icon

    Graphia

     1 like
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    Graphia is a powerful open source visual analytics application developed to aid the interpretation of large and complex datasets.

    License model

    • Free • Open Source

    Platforms

    • Mac
    • Windows
    • Linux
    Graphia screenshot 1

    Graphia Features

    1.  Data visualization
    2.  Bioinformatics

    Graphia VS Cytoscape

     
    Comments about Graphia as an Alternative to Cytoscape
    Guest
    Positive •Oct 18, 2023
    1

    Handles bigger graphs than Cytoscape

    Cytoscape Icon
    Graphia icon
    • Graphia is Free and Open SourceCytoscape is also Free and Open Source

  10. VOSviewer

     4 likes
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    VOSviewer is a software tool for constructing and visualizing bibliometric networks. These networks may for instance include journals, researchers, or individual publications, and they can be constructed based on co-citation, bibliographic coupling, or co-authorship relations.

    6 VOSviewer alternatives

    License model

    • Free • Open Source

    Platforms

    • Mac
    • Windows
    • Linux
    VOSviewer screenshot 1

    VOSviewer VS Cytoscape

     
  11. KeyLines Graph Visualization Toolkit icon

    KeyLines Graph Visualization Toolkit

     4 likes
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    KeyLines is a JavaScript toolkit used by developers to build powerful network visualization applications, quickly.

    39 KeyLines Graph Visualization Toolkit alternatives

    License model

    Application type

    Country of Origin

    • GB flagUnited Kingdom

    Platforms

    • Mac
    • Windows
    • Linux
    • Online
    • Android
    • iPhone
    • Android Tablet
    • iPad
    KeyLines Graph Visualization Toolkit screenshot 1

    KeyLines Graph Visualization Toolkit Features

    1.  Data visualization
    2.  Layout
    3.  Graphs
    4.  Flow Chart
    5.  Geospatial analysis

    KeyLines Graph Visualization Toolkit VS Cytoscape

     

    • KeyLines Graph Visualization Toolkit is the most popular Android, iPhone, iPad & Android Tablet alternative to Cytoscape.

    • KeyLines Graph Visualization Toolkit is Paid and ProprietaryCytoscape is Free and Open Source
  12. Polinode icon

    Polinode

     6 likes
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    Polinode is a tool that makes it easy to perform powerful network analysis. You can either upload your own network data or use the integrated relationship-based survey tool to collect data for you before analyzing and visualizing your networks.

    License model

    Application type

    Country of Origin

    • GB flagUnited Kingdom

    Platforms

    • Online
    Polinode screenshot 1

    Polinode Features

    1.  Real time collaboration
    2.  Change Management

    Polinode VS Cytoscape

     
  13. Neoclipse icon

    Neoclipse

     1 like
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    Neoclipse is a standalone workbench application to interact with Neo4j (database directory or server). It supports Cypher, index searches, visualisation, graph updates.

    License model

    • Free • Open Source

    Application type

    Country of Origin

    • US flagUnited States

    Platforms

    • Windows

    Neoclipse Features

    1.  Graphs
    2.  Layout

    Neoclipse VS Cytoscape

     
  14. GraphXR icon

    GraphXR

     1 like
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    Kineviz GraphXR is a browser-based visualization platform for interactive analysis of big, high dimensional, and or connected data.

    15 GraphXR alternatives

    License model

    • Free Personal • Proprietary

    Application types

    Country of Origin

    • US flagUnited States

    Platforms

    • Mac
    • Windows
    • Linux
    • Online
    • iPad
    • Self-Hosted
    • Software as a Service (SaaS)
    People, objects, locations, and events from a crime dataset`

    GraphXR Features

    1.  Graphs
    2.  Interactive Graph Exploration
    3.  Layout
    4.  OSINT
    5.  Data visualization
    6.  3D visualization
    7.  Bioinformatics
    8.  Graph database

    GraphXR VS Cytoscape

     

    • GraphXR is the most popular SaaS & Self-Hosted alternative to Cytoscape.

    • GraphXR is Free Personal and ProprietaryCytoscape is Free and Open Source
12 of 17 Cytoscape alternatives