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FORG3D

FORG3D is an open source software program that has been developed with C++. FORG3D can be used to visualize different types of data as three-dimensional force-directed graphs.

FORG3D was especially developed to help researchers to interpret and explore complex biological data and to demonstrate how force-directed 3D graphs can be used for this purpose. Nevertheless, FORG3D can also be used to visualize other than just biological data. FORG3D can be used to create and edit force-directed graphs (hence the name, FORG3D, Force-Directed Graph Editor), but users can also write their own scripts/plug-ins that automates the creation of graphs and saves them in the simple text-file format that allows importing of graphs to FORG3D.

You can find additional information about FORG3D from this website, including background, examples and user manual. You can also download the software, including its source code.