Undirected Graph Clusters

The fdp layout program supports edges between nodes and clusters and cluster-to-cluster. The syntax is fairly obvious.
fdp is being actively worked on, so the probability of hitting a bug is higher than with neato. Also the quality of the layouts will be improving.

[Input .gv File] [SVG] [Raster Image]

fdpclust.gv.txt
graph G { layout=fdp e subgraph clusterA { a -- b; subgraph clusterC { C -- D; } } subgraph clusterB { d -- f } d -- D e -- clusterB clusterC -- clusterB }

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