classify.seqs, align.seqs ¿reference or template?


I have observed that at Miseq SOP, both classify.seqs and align.seqs are ran with a “reference” argument, but in their manual entry only a “template” argument is shown on the examples. I thought that maybe they are synonymous, but I tried to ran the same classify.seqs command only changing that word, and I have seen that there are in fact some differences in the output files and log. ¿What is the difference between using “reference” or “template”?.

Thanks a lot

It’s the same thing.