mothur

Generalized UniFrac CRAN Package

Background
I would like to calculate generalized UniFrac distances (1) for a microbial community produced from the MiSeq SOP (2). All of the authors’ example code works (3), but I do not know how to load a tree from Mothur into R. I’ve been playing around with Mothur’s clearcut function, but I have not had success.

Question
What do I need to do to get a tree from the Mothur pipeline that will load like the one in the example code that can be used for UniFrac distance calculations?

References
1: http://bioinformatics.oxfordjournals.org/content/early/2012/06/17/bioinformatics.bts342.abstract
2: http://www.mothur.org/wiki/MiSeq_SOP
3: https://cran.r-project.org/web/packages/GUniFrac/GUniFrac.pdf

What do you mean that you “have not had success”? It could be that your distance matrix is too large to build a tree. If this is the case, then I’d encourage you to use an OTU-based approach instead.

Pat