CyClus3D is a Cytoscape plugin for identifying functional modules in integrated networks composed of multiple interaction types. CyClus3D operates by clustering user-defined 3-node network motifs.
Audenaert, P., Van Parys, T., Brondel, F., Pickavet, M., Demeester, P., Van de Peer, Y., & Michoel, T. (2011). CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks. BIOINFORMATICS, 27(11), 1587–1588.