Greengenes

Commands in mothur
1

Hi everyone,

I have a couple of questions about using the greengenes alignment instead of the silva alignment from the SOP. I have read that when you use greengenes, you will use it with the classify.seqs command, so does that mean that you would skip all of the steps between pcr.seqs and remove.seqs? Or will you use the classify.seqs and then start at the align.seqs command?

Thank you!
-Mara

2

I assume you mean that you want to use greengenes for classification instead of the RDP. In that case, you want to do everything the same except instead of using the RDP file you’d use the greengenes files. There’s really no good reason to use greengenes to align you sequences. It’s a pretty dreadful alignment.

Pat