If a graph is simple, it's easy enough to just look through. For more complex graphs though, it's hard to make sense of if it's not arranged in a way that resembles how developers conceptualize a class or method hierarchy. Understandably, NDepend wouldn't be able to do this automatically.
Can I move graph nodes around by hand? Or alternatively, is there another program that I can export the graph to and rearrange the nodes there?
