tulip

System dedicated to the visualization of huge data sets as graphs
  http://tulip.labri.fr/
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Tulip is an information visualization framework dedicated to the analysis and visualization of relational data. It aims to provide the developer with a complete library, supporting the design of interactive information visualization applications for relational data that can be tailored to the problems he or she is addressing.

It includes the following features:

* 3D visualizations * 3D modifications * Plug-in support for easy evolution * Building of clusters and navigation into them * Automatic drawing of graphs * Automatic clustering of graphs * Automatic selection of elements * Automatic metric coloration of graphs