Do I use the original fasta and count_table files when running get.oturep? … I used a fasta and count_table from early in the mothur run, and got a rep.count_Table and rep.fasta files. Do I use this fasta file to look for BLAST results for the ITS fungal region?

If you are following the SOP’s, you will want, final.fasta, final.names, final.dist, or the equivalent countable and unique_list files.

I followed the SOP most of the way however I am working with the fungal ITS region that does not have a reference alignment therefore I had to stop following the SOP at that point.