@nick-youngblut, I’m not sure of the source of the difference but thank you for flagging it. Weighted UniFrac is deterministic, and the implementations of UniFrac used by QIIME 2 are validated against the original implementation of UniFrac by Cathy Lozupone from PyCogent (unit tests for the version of UniFrac being used by QIIME 2 by default are here). Has anyone in your team followed up with the phyloseq developers about the difference?
Best,
Daniel