Yes, cluster nodes. And yes, subgraphs will be part of one graph. And it will probably do what you want (connecting nodes). I wanted the opposite - connect borders of subgraphs and it was very tricky. If you work on Windows then you will have many graphviz examples in directory C:\Program Files\Graphviz2.22\share\graphviz\graphs, e.g. C:\Program Files\Graphviz2.22\share\graphviz\graphs\directed\clust2.gv which show well how graphviz (well, actually dot, not graphviz: dot.exe -Tpng clust2.gv > clust2.gv.png) renders it.