The reason I would not go clustering tools is that, they cluster based on input parameters, and outputs those which did not meet the criteria as unique. Especially, when one does not know how much similar is the other organism, it is hard to put a similarity cutoff. But in contrast, BLAST computes the similarity and tables the results. So, we could cherry pick those which did not have hit as unique sequences to that particular file. If at all, the user wants, he could still use the output file generated from BLAST file and could put cutoff's and pick up hits he wanted. Nonetheless, I would be happy to hear your points also for choosing clustering techniques.