Hi:

So, after using MetaPhlan, I obtained an abundance table that I would like to analyze.

My main objective is to compare 2 communities, so I'm searching for a pipeline that will allow me to obtain a) alpha-diversity, b) beta-diversity c) Multivariate analysis.

I'm wondering if someone has a bibliography or a tutorial for this, since I've been searching and most of the approaches are for 16S analysis, not shotgun data.