Hi,
I’m new to using mothur and could use a little help. I have generated a whole genome alignment of 20 bacterial isolates using Mugsy. I’m wanting to identify the core genome/alignment using mothur as a fasta file. This paper(http://gbe.oxfordjournals.org/content/5/4/699.full#sec-2) mentions using mothur to do just that, but doesn’t go into details. Any help as to the proper mothur commands and how to use them would be appreciated!