I’m trying to find out what is actually doing. Intuitively it seems clear, but this seems unsatisfying for me.

  • I guess it decides based on the headers which sample it came from. The wiki only tells what the output looks like, but the input is missing.
  • What happens if there are duplications of the headers?

I’m pretty new to mothur (which I mainly want to use via Galaxy). So I want to learn the background of the tools that I’m using.

The command takes a series of individual fasta files, and treats each file as a separate group. Using the code example on the wiki:

mothur >, groups=A-B-C)

mothur would take three input files (sample1.fasta, sample2.fasta, sample3.fasta) and create a single groups file that lists all the sequences in sample1 as belonging to group A, those in sample2 to group B, and sample3 to group C.

If you want multiple files into a single group, I think you can do something like

mothur >, groups=A-B-B)

or if you already have your groups file, the merge.groups command can be used.