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GraphThing - GraphThing is a tool that allows you to create, manipulate and study graphs.
Rocs - Rocs aims to be a Graph Theory IDE for helping professors to show the results of a graph algorithm...
Graphynx - Create weighted and unweighted graphs and run algorithms step by step.
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.
GraphTea - the free and opensource(GPL) software framework to work on graphs and social networks.