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This Stackoverflow question may be helpful:
http://stackoverflow.com/questions/942361/what-is-a-good-network-graph-library-for-language-x
I'm not sure if you're trying to generate graphs by hand or process some existing graph. The question above has graph libraries but also has pointers to some visualization and graph editing tools. You could post-process the yED output to remove the unnecessary information using networkX or similar.
Dan