Sequence Distance WITHIN a group

Hi -
I’m trying to figure out if Mothur can do this. I have sequences with a priori categorical groups, and I want to determine what the divergence is of those sequences within each group (about 100 groups total). Most of the analyses I’ve seen look at distances between groups. For example, I’d like to be able to say that the sequences within group A are X% different while those in group B is Y% different.

Any thoughts? Thanks!

I just submitted this paper :slight_smile: Shoot me an email and I can send the code to you. It’s not likely to wind up in mothur, but I can give you the code.