The MatCompare software provides methods for comparing transcription factor binding site (TFBS) position frequency matrices (PFMs). The user has a choice of using the Kullback-Leibler divergence, the chi squared test or the Fisher-Irwin exact test of similarity.
A stand alone version of the software can be downloaded here
MatCompare can also be downloaded as part of the CREAD package.

Michael Zhang Lab, Cold Spring Harbor Laboratory, all rights reserved
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