PCoA are different between qiime2 and physeq r package.

[Nicholas_Bokulich]

Hi @11132,
This is a known issue with phyloseq: very different weighted unifrac values for qiime2 versus phyloseq · Issue #956 · joey711/phyloseq · GitHub

See also these QIIME 2 forum topics for relevant discussion and description of testing and validation of the UniFrac implementation used in QIIME 2.

Very different weighted unifrac results for qiime2 versus phyloseq

@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

How to tell which UniFrac calculation is correct from different software

Hi @wallacelab, Thank you for joining the form, and for taking the time to perform this assessment and post the exploration! UniFrac is deterministic, and variation in results is unexpected. QIIME 2 uses an implementation of Striped UniFrac. The unit tests for Striped UniFrac are derived from the unit tests for the Fast UniFrac implementation in scikit-bio (which QIIME 2 used previously). These implementations exhibit identical results to the best of our knowledge. The unit tests for Fast UniF…