Python library to convert networks from/to many different formats, like the ones used in Pajek, Cytoscape and other popular graph formats like GML. It also includes support to integrate experimental data to the netowork.
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.
boost_graph tried to wrap the C++ Boost Graphlibrary in Python, providing graph algorithms like Breadth First Search, DFS, Shortest Path, Topological sort. This project is dead (http://bayleshanks.com/pamv1)
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e4Graph is a C++ library and a Tcl binding providing persistent, reliable, cross-platform storage for graph like structures. Please visit http://e4graph.sourceforge.net for more info.