Also sometimes for a directed graph try variants of: neato -Gmode=ipsep -Goverlap=false and maybe -Gsplines=true

Splines don’t scale that well in neato (it builds a huge visiblity graph on all the points of the node polygons) but the others are good.

Sometimes “neato -Gmodel=subset” helps. This changes the node distance model to Jaccard distance. See Figure 5 in www.graphviz.org/documentatio...