Quantifying and estimating the differences between trees with treespace

Comparing trees to differentiate or group them can help researchers to see patterns of evolution. Multiple trees of a single gene tracked across species or strains can reveal differences in how that gene is changing across species. At the core of these approaches are metrics of distances between trees. In this recipe, we’ll calculate one such metric to find pairwise differences between 20 different genes in 15 different species, hence 15 different tips with identical names in each tree. Such similarity in trees is needed to compare and get distances, and we can’t do an analysis like this unless these conditions are met.

Getting ready

For this recipe, we’ll use the treespace package to compute distances and clusters. We’ll use ape and adegraphics for accessory loading and visualization functions. The input data will be 20 files of Newick format trees, each of which represents a...