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Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.
Pajek - Pajek is a lightweight solution developed from scratch by an extraordinary team of developers for the purpose of Large Network Analysis.
NodeXL - Home
Centrifuge - Centrifuge is a complex and highly useful data analysis tool that allows for interactive data exploration.
GraphThing - GraphThing is a tool that allows you to create, manipulate and study graphs.