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there are several methods to detect hierarchical
community structures in networks. However, we couldn't find methods to compare the different obtained hierarchies
(for example, by using different detection methods). Therefore, we
Hierarchical mutual information for the comparison of hierarchical community structures in complex networks
Juan Ignacio Perotti, Claudio Juan Tessone, Guido Caldarelli, Phys. Rev. E 92, 062825 (2015)http://arxiv.org/abs/1508.04388v2
Also, in the introduction of the paper we provide references to different detection methods which can be useful to you as well.
I hope this helps.