Version 0.1.0 BETA
DISCLAIMER: This is a beta-version of JWaRSwap2 and does not have all of the features planned for the final version. It has been tested to an extent that the authors feel confident in its performance, but we cannot guarantee that it is suitable for any purpose whatsoever. Use with caution and stay tuned for the official release.
JWaRSwap2 is a fast, easy-to-use tool for network randomization and network motif discovery. By default, it uses a modified form of the WaRSwap algorithm (Megraw et al., 2013) followed by simple edge-switching to generate random networks sharing the degree sequence of an input network. By combining these two algorithms, JWaRSwap2 combines speed with asymptotically uniform sampling. JWaRSwap2 is designed for motif disovery on directed networks with self-loops allowed and can handle networks with colored vertices.
JWaRSwap2 uses a modified version of subenum (Shahrivari and Jalili, 2015), which handles colored vertices and uses nauty (McKay and Piperno, 2014) to accurately recognize isomorphic subgraphs.
The program is available as a precompiled JAR file here.
Source-code and documentation can be viewed here.
References:
McKay, B.D. and Piperno, A., Practical Graph Isomorphism, II,
Journal of Symbolic Computation, 60 (2014), pp. 94-112, https://doi.org/10.1016/j.jsc.2013.09.003
Megraw, M., Mukherjee, S. & Ohler, U. Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
Genome Biol 14, R85 (2013). https://doi.org/10.1186/gb-2013-14-8-r85.
