Cytoscape alternatives: 3 apps ranked by verified data
Common reasons people leave Cytoscape: interface and terminology are geared to biology, and many analysis features depend on installing separate apps. We ranked 3 alternatives by how directly each one replaces Cytoscape, then by reviews, real visits and how recently each app's facts were checked against its own website. Gephi currently ranks first.
No alternatives match these filters.
Show all 3 alternativesThe best Cytoscape alternative for…
The highest-ranked app in this list for each need.
Best Cytoscape alternative for most people
GephiGeneral-purpose open-source network tool with faster layouts for big social and web graphs.
Best Cytoscape alternative for a free option
yEd Graph EditorFree graph editor for smaller networks where automatic layout and clean diagrams matter most.
Best Cytoscape alternative for a free plan you can upgrade
KumuWeb-based relationship mapping that is much easier for non-specialists to share and present.
Best Cytoscape alternative for open source
GephiGeneral-purpose open-source network tool with faster layouts for big social and web graphs.
Best Cytoscape alternative for self-hosting
KumuWeb-based relationship mapping that is much easier for non-specialists to share and present.
Best Cytoscape alternative for Mac
GephiGeneral-purpose open-source network tool with faster layouts for big social and web graphs.
Best Cytoscape alternative for Windows
GephiGeneral-purpose open-source network tool with faster layouts for big social and web graphs.
Best Cytoscape alternative for Linux
GephiGeneral-purpose open-source network tool with faster layouts for big social and web graphs.
Best Cytoscape alternative for working in the browser
GephiGeneral-purpose open-source network tool with faster layouts for big social and web graphs.
Cytoscape alternatives: common questions
What is the best alternative to Cytoscape?
Gephi ranks first right now. General-purpose open-source network tool with faster layouts for big social and web graphs. Kumu and yEd Graph Editor follow it in our ranking.
Is there a free alternative to Cytoscape?
Yes. Gephi (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 Cytoscape?
Yes: Gephi.
Which Cytoscape alternatives work on Linux?
Gephi and yEd Graph Editor run on Linux.
Why do people switch from Cytoscape?
The complaints we hear most: 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.
How is this list ranked?
Every app is scored with the same published formula: how directly it replaces Cytoscape, reviews (weighted by verification), visits from AppBreakup, how recently its facts were checked against its own website, and reader votes.