CoSE: Compound Spring Embedder
CoSE is an algorithm based on the traditional force-directed layout scheme with extensions to handle multi-level nesting, edges between nodes of arbitrary nesting level, varying node sizes, and other possible application-specific constraints.
A web based demonstration of CoSE is here.
Integrated into Chisio
CoSE algorithm has been implemented in Chisio, a free editing and layout tool for compound or clustered graphs.
Cellular Pathway Layout
CoSE algorithm has also been successfully customized for, and implemented as part of the following pathway visualization software: ChiBE, VISIBIOweb, and PATIKAweb.
U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, "A Layout Algorithm For Undirected Compound Graphs", Information Sciences, vol. 179, pp. 980-994, 2009.