JGraphEd is a Java-based system for exploring properties of graphs. It allows the user to create graphs by pointing and clicking, and then has many different functions which can be performed on the graph (such as depth-first search, canonical ordering, minimum spanning tree, and Dijkstra's algorithm). The application version allows loading and saving of files, so this might make a good environment for creating labs and homework assignments with both the problem-set and the deliverables being JGraphEd documents.

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