The clusterMaker2 plugin for Cytoscape has an implementation of this kind of community clustering. It uses GLay. The plugin hasn't been quite as fast for me as the GLay authors report but I'm content to blame that on my old* Core2 Quad 2.4GHz and/or the massive changes in Cytoscape over the last few years.
*This one came with the lab and was originally used for working with sequencing data. I'm going to use it until it dies and/or catches on fire.