Repository for dependencies between software design artefacts
EMFTrace extends the EMFStore repository by elicitating dependencies between related models of different modeling and programming languages. The explicit recording and modeling of different types of dependencies as traceability links shall support evolutionary changes by impact analysis, early evaluation of quality flaws, and better comprehension. It is an open source project to support the practical application of research results regarding development methods for evolution of software architectures and for software reengineering.
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GraphTK is a graph-generation toolkit. Providing a GUI frontend, it enables you to generate graphs describing build systems (Make, Ant) and API (Java APIs) dependencies. The generated graph data can be stored in common data formats like GraphML or GML. This project is no longer actively developed.
Djinn is a java bytecode static analyser. It can produce various dependencies graphs of arbitrary granularity (jars, classes, packages, etc.) and provide a flexible query engine.
Update 15 apr 2013: I resumed developpement recently, project has moved to https://github.com/fabienbk/djinn