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JGraphT is a free Java class library that provides mathematical graph-theory objects and algorithms. JGraphT supports a rich gallery of graphs and is designed to be powerful, extensible, and easy to use.
JAGAL provides implementations for directed graphs (weighted and unweighted) and varoius types of transition systems as well as utils for graph traversal and modification.
JAGAL builds upon the Java library TOVAL (located at http://sourceforge.net/p/toval). To use JAGAL, make sure the TOVAL library is on the build path.
This library uses and encloses jGraphX (https://github.com/jgraph/jgraphx).
A documentation for JAGAL can be found under http://doku.telematik.uni-freiburg.de/jagal.