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Cytoscape - Cytoscape Official Web Site
GraphThing - GraphThing is a tool that allows you to create, manipulate and study graphs.
Polinode - Polinode is a tool that makes it easy to perform powerful network analysis.
SocNetV - Social Network Visualizer (SocNetV) is a cross-platform, user-friendly free software application for social network analysis and...
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
jsflap - A web-based NFA and DFA construction and testing tool.