# PCoA are different between qiime2 and physeq r package.

**URL:** https://forum.qiime2.org/t/pcoa-are-different-between-qiime2-and-physeq-r-package/17042
**Category:** General Discussion
**Tags:** pcoa
**Created:** [October 12, 2020, 9:59pm UTC](https://forum.qiime2.org/t/pcoa-are-different-between-qiime2-and-physeq-r-package/17042 "2020-10-12T21:59:04Z")
**Posts on this page:** 1
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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [October 13, 2020, 5:39am UTC](https://forum.qiime2.org/t/pcoa-are-different-between-qiime2-and-physeq-r-package/17042/2 "2020-10-13T05:39:53Z")

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Hi @11132,  
This is a known **issue with phyloseq** : [very different weighted unifrac values for qiime2 versus phyloseq · Issue #956 · joey711/phyloseq · GitHub](https://github.com/joey711/phyloseq/issues/956)

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](https://forum.qiime2.org/t/very-different-weighted-unifrac-results-for-qiime2-versus-phyloseq/4591/12):
>
> @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](https://github.com/biocore/scikit-bio/blob/master/skbio/diversity/beta/tests/test_unifrac.py)). 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](https://forum.qiime2.org/t/how-to-tell-which-unifrac-calculation-is-correct-from-different-software/11892/11):
>
> 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](https://www.nature.com/articles/s41592-018-0187-8). The [unit tests](https://github.com/biocore/unifrac/blob/master/sucpp/test_su.cpp) for Striped UniFrac are derived from the [unit tests](https://github.com/biocore/scikit-bio/blob/master/skbio/diversity/beta/tests/test_unifrac.py) for the [Fast UniFrac](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2797552/) 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…

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