I obtained a clustermap from hierarchical clustering of pairwise distances of atoms in an protein alignment. Using a specific cut-off for cluster selection, i found several clusters that "biologically" speaking make sense to me. However, I also obtained one very big cluster that seems to be rather composed of several clusters, which do not appear as single clusters at the cut off i used. So here is my question:
Is it allowed to extract this cluster and cluster this again? By allowed I mean, does it make sense or am I undermining the principal of hierarchical clustering by reclustering?