A multiple maximum common subgraph detection tool for Cytoscape.

CytoMCS is a Cytoscape 3.0 app for computing the maximum common edge subgraph between two or more large networks. The app uses an iterative local search algorithm to find large conserved subgraphs, and is able to detect not only fully conserved edges, but also partially conserved. CytoMCS supports both directed and undirected networks.


The Cytoscape app is available through the Cytoscape app store here:

A standalone command line version is also available here.


First clone and compile the FaithMCS repository:

git clone
cd faithmcs
mvn package

Then clone the CytoMCS repository, install the FaithMCS package locally and compile:

git clone
cd cytomcs
mvn install:install-file -Dfile=/path/to/faithmcs-0.2.jar
mvn package

The compiled Cytoscape 3.0 app can then be found in cytomcs/target/cytomcs-1.1.jar.

Source code

The source code for CytoMCS and FaithMCS is available here:


CytoMCS is licensed under the GPU General Public License v3.0. See for more information.


Larsen, S.J., Baumbach J., 2017. CytoMCS: a multiple maximum common subgraph detection tool for Cytoscape. In Proceedings of the 2017 International Symposium on Integrative Bioinformatics. (In press)