Matlab motif count toolbox
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This a fast, c++ based, motif count toolbox. 
The included functions counts motifs of orders 3 and 4 in binary directed networks 
in the scales of single vertex and the total network.
To view example code run example.m .

The software runs on windows 64 bit, the mex files were compiled with visual studio 2013.
Source files are included. To compile them in different systems enter 
"mex evaluate3motifs.cpp mex3motifs.cpp" for 3 motifs.
"mex Evaluate4motifs.cpp mex4motifs.cpp" for 4 motifs.

The algorithm is detailed in:
Itzhack Royi, Yelena Mogilevski, and Yoram Louzoun. "An optimal algorithm for counting network motifs." Physica A: Statistical Mechanics and its Applications 381 (2007): 482-490. 
Yoram Louzoun's lab: http://peptibase.cs.biu.ac.il/
Royi Itzhack's homepage: http://u.cs.biu.ac.il/~itschar/

This toolbox uses "Lev Muchnik's complex networks toolboox" for preprocessing of the graph data:
http://www.levmuchnik.net/Content/Networks/ComplexNetworksPackage.html