SailMCS is a heuristic algorithm for the multiple maximum common subgraph problem on simple (undirected, unweighted) graphs.

The source code is available at http://github.com/SimonLarsen/sailmcs.

Test data is available here.

Requirements:

• Modern C++ compiler supporting C++11 and OpenMP
• Make
• CMake >= 2.8
• Boost headers
• help2man (optional, used for man page generation)

With all requirements installed, run the following commands:

git clone --recursive https://github.com/SimonLarsen/sailmcs.git
cd sailmcs
cmake . && make

Optionally, you can install the binary and documentation with:

sudo make install

To align three graphs for 10 minutes run:

sailmcs -t 10:00 -o alignment.txt -g mcs.sif graph1.sif graph2.sif graph3.sif

The maximum common subgraph will be written to a file mcs.sif and the table of vertex alignments will be written to alignment.txt.

For a list of supported graph formats see here.

SailMCS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

If you use SailMCS in your research, we kindly ask you to cite the following paper:

Larsen, Simon J., et al. "A simulated annealing algorithm for maximum common edge subgraph detection in biological networks." Proceedings of the Genetic and Evolutionary Computation Conference 2016. ACM, 2016.