The ecological monograph linked below has generalized phylofactorization beyond compositional data (e.g. to presence/absence data, Poisson or multinomial counts, etc.).

The R package now follows the structure of the monograph, and an up-to-date tutorial is available on the "Resources" tab of my personal website (https://www.alexwashburne.com) . Among other things, you can now make much cooler plots highlighting the clades you've found, thanks to the R package ggtree.

Happy science-ing!

https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecm.1353