As is often the way with science published papers can skimp on the details of some of their methods.
I hope to gradually fill this page with step-by-step guides on how to do various things that I have picked up myself over the years, almost all revolving around editing and analysing phylogenetic trees.
I do a lot of my work using the freely-available statistical programming language R and a lot of what follows has an R code implementation.
R has a few key advantages over many standard "canned" packages (e.g. Excel):
1) it is completely free, 2) it is very broadly used in the sciences, 3) it is relatively easily to write code that performs repetitive tasks automatically, 4) it is very powerful and can be used on high performance computing set ups, 5) many of the things you would want to do with it (e.g. read in a phylogenetic tree) already have free libraries of functions to do it and 6) code is run line-by-line so that any errors are quickly located.
Although I try and provide step-by-step instructions a familiarity with R will greatly improve your usage of these pages.
This book comes highly recommended as an introduction to both R and basic statistics.
This book discusses the functions in the APE (Analysis of Phylogenetics and Evolution) library, e.g. reading phylogenetic trees into R.
Currently available methods
Methods planned for the future
- Ancestral character estimation (continuous and discrete characters)
- Time-slicing of phylogenetic trees (geologic time and study time)
- Phylogenetic palaeobiogeography (ancestral area estimates)