Q:

Graphviz allow edge-node overlap

I would like to use graphviz for a project and am unable to get the behaviour I want. I have a graph that I can draw with graphviz just fine, but I also have a version of the same graph that has some extra edges. I would like the second graph to be drawn with the nodes in the same positions as the first one and the edges in the same positions, but the new edges to be drawn without avoiding any overlap with nodes.
To get a better idea of what I want, imagine a Powerpoint slide with a graph and then on the next slide the same graph with these extra edges that appear on top of the first graph, wihtout modifying the look of the old parts of the graph. That is the effect I want.
I think the effect could be achieved by having some edges ignore any overlapping constraints. I could not figure out how to control the overlap between edges and nodes for particular edges (or even for all edges). 
Any ideas?

A:

You can get dot to output another .dot file, with positions assigned to all elements, via dot -Tdot (or maybe dot -Txdot).  Add your additional edges to that file, and run it through dot again to produce your second graph.

