Hey Pat,
I’ve been using a chopped silva.bacteria.fasta to the region I align to, and I now see this in the MiSeq SOP (i have some good intuition!) . I’m wondering if this approach would aid in the classify.seqs part of the pipeline? I do see no problem with classifying producing any large files or taking too long, but it was just a thought.
maybe a new command in mothur “answer.question”
Shaun