The commands referenced below are all part of special phylogenetic packages in R, not the basic R install. Be sure that you have installed and loaded the packages containing the commands referenced below before continuing. For example:
This loads the package ape and its required packages gee, lattice and ade4 into your R session.
How do I input data corresponding to the tips of my phylogeny into R?
First, assemble your data into a tab delimited text file (this can be done, for example, in a simple text editor or in MS Excel)