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The H3Viewer library provides layout and interactive navigation of node-link graphs in 3D hyperbolic space. The library can handle quite large graphs of over to 300,000 edges quickly and with minimal visual clutter. The hyperbolic view allows the user to see a great deal of the context around the current focus node.
This library is a slightly updated version of the one used in the SGI product Site Manager.
See also Young Hyun's Walrus software, which is a very nice Java3D implementation of these algorithms.