Handling phylogenetic trees in R
For this meeting, my goal is to introduce you to how phylogenetic trees are coded as text files, how to get them into R, how they are stored in R, and how to do some basic plotting and manipulations. We will use the
ape package, although I will briefly discuss other packages that people might want to use. I will be speaking from the perspective of someone who uses phylogenetic trees as a data resource, and thus will not be talking about the generation of trees from raw molecular or morphological data.
Prior to the meeting
- Please install the
apepackage (available through CRAN).
- Download the following files and put them in your working folder
- [Paradis (2012) Analysis of Phylogenetics and Evolution with R. 2nd edition. Springer.] (http://www.springer.com/gp/book/9781461417422)
- Felsenstein (2004) Inferring Phylogenies. Sinauer.
apepackage project page