I ran pick_closed_reference_otus.py over the hmp dataset and acquired the biom file and the otu tables.
Now I need to run certain diversity analysis on the object. However the phylogenetic tree object in the phyloseq object is empty.
Error in access(physeq, "phy_tree", errorIfNULL) :
phy_tree slot is empty.
I understand that I never entered a phylogentic tree to my biom file.
Now the question is how do I add green genes phylogenetic trees ( gg/99_otus.tree) to the phyloseq object?
It should be straight forward but I can't find a function for reading the tree file into phyloseq.
Thanks in advance :)