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The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.
The main home page of the CDK is now at: http://cdk.github.io
Gato (Graph Animation Toolbox): Animate graphalgorithms for example for computing shortest paths, minimal spanning trees, maximum flows or maximal cardinality or weight matchings. Create your own animations using the Animated Data Structures (ADS).
G.A.V. (Graph Algorithm Visualizer) is a tool that visualizes algorithms from graph theory. A step-by-step visualization from each different algorithm allows the user to understand the particular algorithm very easily.
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.