Clustering based on QCUT, HQCUT, MCL, MCODE.
Categories: clustering, graph analysis
CommFinder is an open source community finder plugin that incorporates two efficient heuristic algorithms: Qcut and HQcut developed as a plugin for Cytoscape. The tool also includes MCL and MCODE, both widely used in community-finding. Key features of the tool: **Qcut algorithm**: Efficient community finder algorithm for large and relatively dense networks. The algorithm does not require any parameters. **HQcut algorithm**: Recursive algorithm detecting communities at a finer level. The algorithm uses minz and minq parameters for higher accuracy. Its accuracy is largely invariant for 10 ≥ minz ≥ 2 and is the best for 0.35 ≥ minq ≥ 0.3. The algorithm solves the resolution limit problem. **Algorithm comparison**: The plugin enables users to run different algorithms (Qcut, HQcut, MCL, MCODE) and compare their results side by side. **Fast**: Qcut, HQcut and MCL algorithms are implemented in MATLAB, hence fast and efficient especially when run against a very large and sparse network. **Color attribute**: After running the algorithm, the communities obtained from the network are uniquely colored for users to easily identify different communities within the network. The user will also have an option to change the color and/or shape of the community if needed. **Sorting capabilities**: Users will be able to sort the communities displayed in the result panel by: Size, Degree Ratio, or Connectivity.
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