Rooting Unifrac Trees in phyloseq Objects

The method of rooting trees described in the post “Unifrac and Tree Roots” is now included in QsRutils beginning with version 0.3.2 as function root_phyloseq_tree. Given a phyloseq object with an unrooted tree, it returns the same type of phyloseq object with the tree rooted by the longest terminal branch.

Unifrac and Tree Roots

Unifrac distances have the attraction of including phylogenetic relatedness, based on a tree of the representative sequences, in the distances among samples calculated from an OTU table. FastTree is the usual method of choice in generating the tree, although USEARCH also provides a method. Both methods calculate unrooted trees, and calculation of Unifrac distances requires a rooted tree. The problem arises in how to best root the tree. I found a discussion of the problem on the phyloseq GitHub site ( Continue reading “Unifrac and Tree Roots”