The Cytoscape plug-in is an application of the ModuLand method family ([http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0012528 PLoS ONE, 7, e12528]) determining and visualizing overlapping network modules (clusters/communities) by calculating the assignment strength of each node to each discovered module. The plug-in builds the hierarchy of network modules, where meta-nodes of the higher layer are the modules of the lower layer. The plug-in also calculates a number of topological measures such as community centrality, bridgeness and overlap, characterizing the centre of modules, as well as intermodular nodes between two or more modules, respectively.
The plug-in is further described here: Szalay-Beko, M., Palotai, R., Szappanos, B., Kovács, I.A., Papp, B. and Csermely, P. (2012) ModuLand plug-in for Cytoscape: extensively overlapping network modules, community centrality and their use in biological networks. Bioinformatics, 28, 2202-2204, [http://arxiv.org/abs/1111.3033]