AppBreakup
Submit an app

Gephi alternatives: 3 apps ranked by verified data

Facts checked Nov 1, 2026AppBreakup editorialHow we rank

Common reasons people leave Gephi: steep learning curve for newcomers, and java desktop app that can feel dated and unstable. We ranked 3 alternatives by how directly each one replaces Gephi, then by reviews, real visits and how recently each app's facts were checked against its own website. Cytoscape currently ranks first.

Quick comparison

#AppPricingOpen sourcePlatformsVerified factsScore
1Cytoscape logoCytoscapeOpen sourceYesWindows, macOS, Linux +14 of 466.5
2yEd Graph Editor logoyEd Graph EditorFreeNoWindows, macOS, Linux +14 of 452.6
  1. Cytoscape logo

    1. CytoscapeTop pick

    Best for: Biologists and data scientists analyzing interaction networks alongside their own data

    Open sourceWindows, macOS, Linux, Web

    66.5

    score / 100

    Why switch from Gephi

    Open-source network analysis platform with hundreds of apps, especially strong for biological data.

    Pros

    • Large app ecosystem for clustering, statistics and domain-specific tools
    • Scriptable from R and Python
    • Free and open source under the LGPL
    • Strong support for biological data formats and pathway databases

    Cons

    • Interface and terminology are geared to biology
    • Many analysis features depend on installing separate apps
    • Java desktop app that can be heavy on large networks
    Visit Cytoscape Details and reviews
    How this score is calculated
    Editorial fit ×0.3100
    Reviews ×0.363
    Clicks (90 days) ×0.150
    Freshness ×0.1585
    Votes ×0.150

    0 counted reviews, 0 up and 0 down votes. Full formula

    Is Cytoscape a good Gephi alternative?

    Verified facts

    4 of 4 verified
    License
    LGPL
    Checked Nov 1, 2026cytoscape.org(opens source in a new tab)
    Apps
    Over a hundred third-party apps
    Checked Nov 1, 2026cytoscape.org(opens source in a new tab)
    Web version
    Cytoscape Web
    Checked Nov 1, 2026cytoscape.org(opens source in a new tab)
    Owner
    Cytoscape Consortium (nonprofit)
    Checked Nov 1, 2026cytoscape.org(opens source in a new tab)
  2. yEd Graph Editor logo

    2. yEd Graph Editor

    Best for: People who need to lay out large graphs or network diagrams automatically

    FreeWindows, macOS, Linux, Web

    52.6

    score / 100

    Why switch from Gephi

    Free graph editor with good automatic layouts for smaller diagrams and hand-drawn networks.

    Pros

    • Excellent automatic layout algorithms
    • Builds diagrams from Excel or XML data
    • Free on Windows, macOS and Linux
    • Browser version available

    Cons

    • Dated Java interface
    • No real-time collaboration
    • Closed source despite being free
    Visit yEd Graph Editor Details and reviews
    How this score is calculated
    Editorial fit ×0.346
    Reviews ×0.363
    Clicks (90 days) ×0.150
    Freshness ×0.15100
    Votes ×0.150

    0 counted reviews, 0 up and 0 down votes. Full formula

    Is yEd Graph Editor a good Gephi alternative?

    Verified facts

    4 of 4 verified
    Price
    Free
    Checked Oct 29, 2026yworks.com(opens source in a new tab)
    Platforms
    Windows, Unix/Linux, macOS
    Checked Oct 29, 2026yworks.com(opens source in a new tab)
    Data import
    Excel (.xls) or XML
    Checked Oct 29, 2026yworks.com(opens source in a new tab)
    Browser version
    yEd Live
    Checked Oct 29, 2026yworks.com(opens source in a new tab)

The best Gephi alternative for…

The highest-ranked app in this list for each need.

Cytoscape logo

Best Gephi alternative for most people

Cytoscape

Open-source network analysis platform with hundreds of apps, especially strong for biological data.

yEd Graph Editor logo

Best Gephi alternative for a free option

yEd Graph Editor

Free graph editor with good automatic layouts for smaller diagrams and hand-drawn networks.

Kumu logo

Best Gephi alternative for a free plan you can upgrade

Kumu

Browser-based relationship mapping that is easier to share and collaborate on, free for public maps.

Cytoscape logo

Best Gephi alternative for open source

Cytoscape

Open-source network analysis platform with hundreds of apps, especially strong for biological data.

Kumu logo

Best Gephi alternative for self-hosting

Kumu

Browser-based relationship mapping that is easier to share and collaborate on, free for public maps.

Cytoscape logo

Best Gephi alternative for Mac

Cytoscape

Open-source network analysis platform with hundreds of apps, especially strong for biological data.

Cytoscape logo

Best Gephi alternative for Windows

Cytoscape

Open-source network analysis platform with hundreds of apps, especially strong for biological data.

Cytoscape logo

Best Gephi alternative for Linux

Cytoscape

Open-source network analysis platform with hundreds of apps, especially strong for biological data.

Cytoscape logo

Best Gephi alternative for working in the browser

Cytoscape

Open-source network analysis platform with hundreds of apps, especially strong for biological data.

Gephi alternatives: common questions

What is the best alternative to Gephi?

Cytoscape ranks first right now. Open-source network analysis platform with hundreds of apps, especially strong for biological data. Kumu and yEd Graph Editor follow it in our ranking.

Is there a free alternative to Gephi?

Yes. Cytoscape (open source), Kumu (free plan + paid) and yEd Graph Editor (free) have a free option. Check each app's verified facts for current plan limits.

Is there an open-source alternative to Gephi?

Yes: Cytoscape.

Which Gephi alternatives work on Linux?

Cytoscape and yEd Graph Editor run on Linux.

Why do people switch from Gephi?

The complaints we hear most: steep learning curve for newcomers; java desktop app that can feel dated and unstable; no real-time collaboration.

How is this list ranked?

Every app is scored with the same published formula: how directly it replaces Gephi, reviews (weighted by verification), visits from AppBreakup, how recently its facts were checked against its own website, and reader votes.