Phylogenies and trees.

Abstract

Abstract Several packages have been developed to allow R-users to work with phylogenetic trees, something that most biologists will need to do at some point in their careers. The most basic is the ape package, which stands for Analysis of Phylogenetics and Evolution. This chapter gives some of the basics of handling 'trees' in R and show things that can be calculated with them. Phytools, another package with extra capabilities, are also introduced in this chapter. Insects are given as examples.