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Cytoscape - Cytoscape Official Web Site
LucidChart - LucidChart is the missing link in online productivity suites. LucidChart allows users to create, collaborate on, and publish attractive flowcharts and other diagrams from a web browser.
Polinode - Polinode is a tool that makes it easy to perform powerful network analysis.
draw.io - Online diagramming application
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
yEd - yEd is a free desktop application to quickly create, import, edit, and automatically arrange diagrams. It runs on Windows, Mac OS X, and Unix/Linux.