@gregcaporaso Thank you very much, that was very helpful. I have tested this approach and it does work after importing feature table and tree.
To the use of amino acids in qiime: The amino acid sequences are from the same protein, in this case MCR from the methanogenesis pathway. I am very interested in functional genes (other than MCR, NOS, NIR, AMO,...) and, for the purpose of high conservation, it made sense to me to conduct classification and diversity analyses on the amino acid level for these genes. Does anybody have more potential benefits from using amino acid sequences to look at?
Thanks for your input!
cheers,
steffen