For instance, I am trying to analise the diversity of each phylum in a microbial community. It would make it easier if I could get a list of all OTU@0.1 or OTU@0.03 that are derived from a given OTU@0.2.
this is such a great idea that it’s already on the list 
Hi Pat, thnx for getting that into the new version. It will also be usefull to get, instead of the list of sequences in each OTU, the OTU numbers. So that I know, for instance, that that from OTU 1 at 0.03 difference I am getting OTUs 1,2,3 at 0.01 difference. I think that would make a more readable file and you can then use the list file to get the sequences for the OTUs that interest you.
And on the same note, when I open the .list file with Excell, the first thing I do is add running numbers in row 1, from 1 to the number of OTUs in the highest similarity I am looking at so that the OTUs are numbered in order of appearance. It would be nice if that row was added automatically to the file.