TOOL ★
Cytoscape logo

Cytoscape

Cytoscape Desktop (Cytoscape 3.x)

Convert from any graph formatto Cytoscape Convert from Cytoscapeto any other format

Cytoscape is an open-source platform for visualising complex networks, popular in bioinformatics.

Repository cytoscape.org

Visual Tool

Graph Formats(Input & Output)

XML FORMAT ★
GraphML
TEXT FORMAT ★
GML
JSON FORMAT ★
Cytoscape JSON logo
Cytoscape JSON
Cytoscape.js JSON
XML FORMAT
XGMML

Input Formats

XML FORMAT ★
Excel
Microsoft Excel
XML FORMAT ★
SBML logo
SBML
TEXT FORMAT ★
SIF
Cytoscape SIF (Simple Interaction Format)
TEXT FORMAT ★
Delimited Text
XML FORMAT
BioPAX
JSON FORMAT
Cytoscape CX2 logo
Cytoscape CX2
TEXT FORMAT
Nested Network
Nested Network Format

Frequently Asked Questions

What graph file formats does Cytoscape support?

See the list on this page — it shows every format Cytoscape can read, write and display.

How do I import a graph into Cytoscape?

Convert your file to a format Cytoscape can read, then open it in Cytoscape. Use GraphInOut to get a Cytoscape-compatible file in seconds.

How do I convert a file so Cytoscape can open it?

Use the convert links above — upload or paste your graph, pick a format Cytoscape accepts and download the result, right in your browser.