Extracting and working with subtrees using ape
A common but often frustrating task is cropping trees to look at a section in a new, clearer context or combining them with another tree in order to present two distant clades more clearly. In this short recipe, we’ll look at how easy it can be to manipulate trees- specifically, how to pull out a subtree as a new object and how to combine trees into other trees. We’ll use the ape package, the phylogenetic workhorse in R that will give us functionality for completing those tasks easily.
Getting ready
We’ll need a single example tree – the mammal_tree.nwk file in the rbioinfcookbook package will be fine. All the functions we require can be found in the ape package.
How to do it…
Extracting and working with subtrees in ape can be executed using the following steps:
- Load the library and tree:
library(ape)tree_file <- fs::path_package( "extdata", "...
