FlashMotif is software for finding statistically significant colored motifs with analytically derived p-values. FlashMotif uses the GLabTrie algorithm for counting occurrences of colored motifs in a graph and implements an analytical model to assess motifs significance without generating random graphs. FlashMotif works on both directed and undirected networks and can handle induced and non-induced injective and multiset topological colored motifs with color-topology dependency or independency.

Before downloading, be sure to have Java installed (version 8 or more).


JAR file of FlashMotif :


JAR file of the software for reproducing experiments (comparison between simulation-based and analytical model):


Source code

JAVA source code for FlashMotif and AnalyticalRepro:


Auxiliary files

Sample networks:


Lists of all undirected topologies with 3 to 8 nodes and all directed topologies with 3 to 5 nodes:



To run FlashMotif or AnalyticalRepro JAR files please refer to the README.txt files contained in the relative ZIP archives.

If you use FlashMotif for reasearch purpose, please cite the following papers:

  • Micale G, Giugno R, Ferro A, Mongiovì M, Shasha D, Pulvirenti P (2018). Fast Analytical Methods for Finding Signicant Colored Graph Motifs. Data Mining and Knowledge Discovery, 32(2), pp. 504-531, doi:10.1007/s10618-017-0544-8. (Link)

  • Mongiovì M, Micale G, Ferro A, Giugno R, Pulvirenti A, Shasha D (2018). gLabTrie: A Data Structure for Motif Discovery with Constraints. Graph Data Management: Fundamental Issues and Recent Developments. Springer, pp. 71-95, doi:10.1007/978-3-319-96193-4_3. (Link)


Giovanni Micale
Dept. of Clinical and Experimental Medicine
University of Catania
Rosalba Giugno
Dept. of Computer Science
University of Verona
Alfredo Ferro
Dept. of Clinical and Experimental Medicine
University of Catania
Misael Mongiovì
Dept. of Mathematics and Computer Science
University of Catania
Dennis Shasha
Dept. of Computer Science
Courant Institute of Mathematical Sciences
New York University
Alfredo Pulvirenti
Dept. of Clinical and Experimental Medicine
University of Catania


If you have any trouble with the software or you want to report any bug, please contact: gmicale@dmi.unict.it and apulvirenti@dmi.unict.it