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GraphThing - GraphThing is a tool that allows you to create, manipulate and study graphs.
UCINET - UCINET for Windows is a software package for the analysis of social network data.
JFLAP - JFLAP is software for experimenting with formal languages topics including nondeterministic finite...
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
Rin'G - Download Rin'G - A non-intrusive tool for the study of graph algorithms
Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.