MOTIVATION: Network biology has emerged as a powerful tool to uncover the organizational properties of living systems through the application of graph theoretic approaches. However, due to limitations in underlying data models and visualization software, knowledge relating to large molecular assemblies and biologically active fragments is poorly represented. RESULTS: Here, we demonstrate a novel hypergraph implementation that better captures hierarchical structures, using components of elastic fibers and chromatin modification as models. These reveal unprecedented views of the biology of these systems, demonstrating the unique capacity of hypergraphs to resolve overlaps and uncover new insights into the subfunctionalization of variant complexes. AVAILABILITY AND IMPLEMENTATION: Hyperscape is available as a web application at http://www.compsysbio.org/hyperscape. Source code, examples and a tutorial are freely available under a GNU license. CONTACTS: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.