mothur

Different results from parsimony and unifrac.unweighted/unifrac.weighted

Dear all,

Hope we have all enjoyed a wonderful Thanksgiving holiday.

Here I have a question about the parsimony and unifrac.unweighted/unifrac.weighted commands. In the Mothur SOP, the results of the commands of parsimony, unifrac.unweighted,
and unifrac.weighted are the same: There was clearly a significant difference between the clustering of the early and late time points.

However, when I ran my own data, I found that:
–The parsimony results indicate that there is no significant difference.
–The unifrac.unweighted/unifrac.weighted results indicate that: The difference is significant.

I understand that the parsimony ignores the branch length and unifrac.unweighted/unifrac.weighted command does. However, I am still not sure how to appropriately interpret the results.

Thanks!

Yours,
Chiqian

As you’ve noted, the tests test different things. You should only pick one test and then report the result. I would never recommend using unifrac.unweighted since it is highly sensitive to undersampling. I’d probably put more value on having the branch length included.

Pat

Thanks a lot for the clarification, Pat. I will then focus on the results from the unifrac.weighted command. Thanks.