classify.otu vs classify OTU representative sequence

Hi there,

In order to get a consensus taxonomic classification of an OTU, normally you would use the classify.otu function. However, you could also get a representative sequence from the OTUs (using Get.oturep with the distance method) and classify this sequence. Then you could perhaps consider this classification as an “OTU classfication”. Can somebody think of any reason that would make the second option better?

We discuss that here:

By doing the representative sequence you may get lucky/unlucky with that single sequence in getting a taxonomy that is not representative of the other sequences in the OTU. I’d stick with classify.otu.

Thanks for that Patrick!