# Comparison of environment by UniFrac

**URL:** <https://forum.mothur.org/t/comparison-of-environment-by-unifrac/2937>\
**Category:** Theory behind mothur\
**Created:** [July 30, 2016, 3:56am UTC](https://forum.mothur.org/t/comparison-of-environment-by-unifrac/2937 "2016-07-30T03:56:00Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![yu62](https://avatars.discourse-cdn.com/v4/letter/y/b2d939/32.png) [@yu62](https://forum.mothur.org/u/yu62)\
**Post date:** [July 30, 2016, 3:56am UTC](https://forum.mothur.org/t/comparison-of-environment-by-unifrac/2937/1 "2016-07-30T03:56:00Z")

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Hello,

I am a bit confused by the use of UniFrac in the OTU-based analysis in the MiSeq SOP ([http://www.mothur.org/wiki/MiSeq\_SOP](http://www.mothur.org/wiki/MiSeq_SOP)).  
As I understand, the original definition of UniFrac is based on the phylogenetic tree of OTUs; To compare different samples, a sample name is assigned to different OTUs; To compare different environments or treatments, a certain environment name is assigned to different OTUs.

In the MiSeq SOP, you used the dendrogram of different samples (after calculating Yue & Clayton dissimilarity index), not a phylogenetic tree of OTUs, as the input for the UniFrac to compare environments or treatments (so the tree shows the relationship among samples, not among sequences).  
I was searching for a paper which used this strategy to compare environments but I have not been able to find any.

Do you think it is still a valid method to compare different environments (in that case could you introduce some papers which followed this strategy, if you know any)? Or should I rather follow the original definition by assigning a certain environment to each OTU and conduct the phylogeny-based UniFrac? (or alternatively compare each sample by phylogeny-based UniFrac and conduct anosim to see the significance of clustering?)

I have a total of 16 different samples from 4 different environments and would like to see if there is any significant effect of environments.

I would appreciate if you could answer these questions.

regards,  
yu62

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [August 1, 2016, 1:22pm UTC](https://forum.mothur.org/t/comparison-of-environment-by-unifrac/2937/2 "2016-08-01T13:22:23Z")

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In the SOP we do it as a statistical test to compare groups based on a tree constructed using samples where the tree is from a beta-diversity index and we also do it to calculate distances based on the sequences in each sample

Pat