Core genome


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( 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!

Huh. That’s funny, I have no idea. Sorry!