One can find the (probabilistic) distance between two HMMs (a distance similar to the Kullback-Leibler measure) using the KullbackLeiblerDistanceCalculator class ^[5].

This class generates n long observations sequences of length l using one HMM and finds their probabilities using the other. Parameters n and l can be set using the setNbSequences and setSequencesLength methods.

Pay attention to the fact that this distance measure is not symetric; see the code documentation for more details.