For those interested:

The code that computes the clusters can be found in the Python script: aux/cluster.py.

This uses the 'ward' cluster method from SciSciPy. Other cluster algorithms are available. See http://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html#scipy.cluster.hierarchy.linkage

The python code can be changed to a different algorithm or the more adventurous can write their own cluster algorithm!