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Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
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.
Wandora App - Wandora is a general purpose information extraction, management and publishing application based on...
draw.io - Online diagramming application
Linkurious - Search and visualize your graph data through a simple web-based interface
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.