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The Deimos Project is a Java-based game development library collection. Includes Vertex Modeler, a 3D modeler that lets you programatically define models using Javasourcecode. The modeler is also a simple scene graph API.
Muli3D is a rendering library which implements features of current graphics hardware in software. The focus is on ease of use and clear code; therefore Muli3D is best suited for research and teaching.