The syllabus (mostly the schedule) will be updated throughout the semester. You can see it as a PDF or RMarkdown file; I have also embedded it below. This site sometimes takes some time to refresh: you can also see the syllabus here.

Phylogenetic Methods (PhyloMeth). Spring 2017

UT students may sign up at EEB 603, CRN 30253 (grad students) or EEB 504, CRN 31819 (advanced undergrads)

Syllabus version: 03:12 PM, 21 March, 2017

Instructor: Brian O’Meara (

Course website:

Office Hours (446 Hesler) by appointment.

Anonymous feedback This is the first time the course is being run, and it’s taught in a very different way from most courses. There is a lot that will go wrong. Let me know what’s not working while it can still improve.

What you will learn

This is a modern class in phylogenetic methods. You will learn how to get data, build a tree, use comparative methods, and how to make new methods. More importantly, you will learn why to do all this.


  • A laptop on which you can install software (have root / admin access)
    • It’ll be easiest if this is a Mac; less easy is Linux; Windows will be hard
  • A question and some data to answer it
  • GitHub account
  • Gitter
  • R
  • And other software we’ll learn about during the course

I am writing a textbook as part of the course * HTML version * PDF

It will be updated as we go, so check back frequently.


Grading will be based on effort and performance. Some of the things will be harder for some students than others just given differences in what they’ve been exposed to so far, and I don’t want to penalize students who are less skilled at R, for example. But I do require that you put in work on this class: work through the exercises, think about the papers, etc. Much of the homework is chewy, so it will take some thought to get through, and you might not be able to do all of this. That’s ok.

  • EEB603 final project will be done solo (though consulting is ok)
  • EEB504 final project will be done in pairs


The class is flipped: rather than me droning at the front of the room, I’ll be releasing videos online for you to watch. They will be linked to from this syllabus. In class, talk about what was not clear from the videos about methods, and we’ll dig into that. We can also work on problematic parts of the exercises (you should do most of them before class) and talk about papers.

Online option

There is an online option, as well. In this second running of the class, I’m not seeking to give out credit, but online visitors are encouraged to sign up.


Course made possible by: NSF CAREER grant to O’Meara & ongoing support from the Department of Ecology & Evolutionary Biology, U. of Tennessee, Knoxville.