Hi Tiago,

Thanks for your quick reply! You were right - the algorithm just didn't converge to anything meaningful: http://www.ebi.ac.uk/~spivakov/testX/full_graph2.png

This is a hard problem to solve in general. It is usually the case that you should have some insight on the total number of communities, and AFAIK there is no known reliable method which will give you this information easily. If your networks are not too large, you can try increasing n_spins values, and stop if the modularity no longer changes appreciably.

Thanks for your advice! My networks are large, so I can't really afford multiple iterations... I have so far also tried the MOSES tool that is quite fast, but the downside (for me) is that it produces overlapping communities and that the granularity is too small for my liking...

Cheers, Mikhail