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GUESS, or the Graph Exploration System, is a system and language for visualizing and manipulating graph structures and creating new visualization applications.
GRINEdit is a graph, relation, interaction, network editor.
The graph visualizer 'graphviz' is very popular but it is not interactive.
The project aims to make interactive graphviz.
C++ and Python based open source graphvisualization and analysis software, primarily intended for use in the analysis of social networks (other applications are also conceivable).
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A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.
bitHull is a Simple unstructured data store-and-share mechanism. It is part experimental graph-based task/note/idea management system and part data aggregator.
Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.