Does tree for unifrac tree to be rooted?

I made a neighbor joining tree in ARB of only my sequences, without any root. Can this be used for unifrac?
According to the original papers, the tree needs to be rooted, but there is no special mention (as far as I can see) of this in mothur.
Also, does the tree only have to my sequences, or also contain other sequences (not in group file). In one of the analysis examples, sequences was added to the Hugenholtz tree in ARB and the tree was exported, but no mention of rooting or if the whole tree was exported, or only the sequences being analyzed…
Thanks for your help!

mothur roots the tree for you

Is this also true for the clearcut command? I too would like to use Unifrac and I want to confirm that the tree I’m uploading is rooted.
I used merge.files to combine my alignment files, should I add an outgroup to the merged files prior to using clearcut?
Thank you,

yup, you should be fine using clearcut and then the unifrac commands within mothur.


Only for curiosity… since mothur roots the tree for you, if one creates a rooted tree elsewhere (e.g. RAxML) to input in any of mothur’s unifrac cmds, would it re-root the tree or would it be happy with with the existing root?


It would use the existing root that’s in the tree.