I was running the classify seqs. command
classify.seqs(fasta=spore.trim.unique.good.filter.unique.precluster.pick.fasta, template=trainset6_032010.rdp.fasta, taxonomy=trainset6_032010.rdp.tax, cutoff=80, processors=2)
and at the end of the Mothur run I received a warning that some of the sequences may be reversed. However, I did use the flip parameter in the alignment to try to correct this problem. We looked in the accnos file that indicates which sequences are reversed and it appears that there are not that many of them so we were wondering if we could simply remove these sequences or continue on and Mothur would just disregard these sequences that are in reverse.