I have a basic question.
What differences are there between the representative sequence and the consensus sequence of same OTU number?
If I construct the NJtree from the sequences, which sequences should I choose?
Thank you for answering, in advance^^
The consensus sequence is not a real sequence - it’s the consensus of all the sequences in the OTU. The representative sequence is the sequence that is the shortest distance to all of the other sequences. I would foresee using the representative sequence as you describe and perhaps the consensus sequence for things like primer/probe design