Hi Colin,
Thanks for your answer.
I will sure try the MAFFT strategy. Perhaps it will indicate us that using a different set of primers could improve our taxonomy classification.
A few hours ago, I found this thread where @llenzi suggests to add the sanger sequences manually into the greengenes database, creatinbg a taxonomy with a distinct name so it is easy to spot after taxonomical classification.
Given that I have several colonies with sanger sequences for each of my individual species, would it be possible to generate a series of consensus seqs and then introduce them manually into the data base as suggested in that thread?
So far I have been following the moving pictures tutorial, but I have to admit that the clawback and taxonomic weights from the tutorial you suggested is really interesting.