BIOL 848 Phylogenetic Methods

This course covers state-of-the-art methods for reconstructing phylogenies. We will cover the theoretical basis for different phylogenetic analyses and learn how to use some of the software packages available for conducting these analyses. Inferences that rely heavily on phylogenetic trees (eg. analyses of character evolution, divergence time estimation, and studies of diversification rates) will also be covered.

The syllabus is available as a pdf from this link.

I will post pdfs here throughout the semester. I will post the source code for my own notes and some slides to a GitHub repository, but much of the lecture is presented on the board. Bear in mind, that a great deal of the content will be given on the board, and my typed notes may be minimal for those sections of the lectures - make sure that you take good notes!

Some links

Felsenstein's Inferring Phylogenies book is highly recommended for the course.

His list of phylogeny programs is also very helpful.

The website for the Workshops on Molecular Evolution is a good source of lecture slides, software tutorials, and general information.


Date Link
Aug-20 Slides: BIOL848-lec1-IntroStats.pdf
Aug-23 Slides: BIOL848-lec2-IntroInference.pdf
Homework: BIOL848-homework1-splits.pdf
Aug-25 Slides: BIOL848-lec3-Inference.pdf
Aug-27 Notes: BIOL848-lec4-SplitCompatibility-notes.pdf
Homework: BIOL848-homework2-newick.pdf
Aug 29 Notes: BIOL848-lec5-StatInference-Notes.pdf
Aug 31 Notes: BIOL848-lec6-ML-CompatModel-Notes.pdf
Homework: BIOL848-homework3-charcompat.pdf
Sep. 7 Lab: BIOL848-lab1-UnixIntro.html
Sep 8. Notes: BIOL848-lec7-ML-MPModel.pdf
Sep. 15 Lab:BIOL848-lab2-paupNEXUSMesquite.html
Sep 17. Notes: BIOL848-lec7-ML-MPModelAlgorithms.pdf
Homework: BIOL848-homework4-parsimony.pdf
Sept. 20 Slides: BIOL848-lec8-Searching.pdf
Sep. 22 Lab: BIOL848 lab3 Tree Searching
Sept. 24 Slides: BIOL848-lec9-Distances.pdf
Sept. 29 Lab: lab4-Distances
Homework: BIOL848-homework5-distances.pdf
Oct. 4 Slides: BIOL848-lec10Models.pdf
Oct. 6 Slides: BIOL848-lec11ML.pdf
Oct. 6 Lab: lab5-Models
Homework: BIOL848-homework6-ML.pdf
Oct. 7 Slides: BIOL848-lec12RateHet.pdf
Oct. 13 Slides: lab6Sim.html
Oct. 20 Lab:garliExercise.html
Oct. 25 Slides: lecture 14 slides (pdf)
Oct. 27 Slides: lec16Bootstrapping.pdf
Oct. 27 Lab: lab7 Testing
Oct. 29 Slides: BIOL848-BayesIntro.pdf
Nov. 1 Slides: BIOL848-BayesSecond.pdf
Nov. 3 Lab: MrBayes Lab. The algaemb datafile is here.
The jc.nex datafile is here.
The mac executable is here. An old version is here
Nov. 8 Slides: BIOL848-lec18-BayesFactors.pdf
Nov. 10 Slides: BIOL848-lec19-AncStates.pdf
Nov. 10 Lab: 09-Mesquite.html
Nov. 12 Slides: BIOL848-lec20-CharEvol.pdf
Nov. 17 Tracy Heath's Slides:
Nov. 16 Lab: this week we are going to work through the BEAST tutorials
Nov. 22 Slides: BIOL848-lec22-MorphologicalCharacters.pdf
Dec 1: Lab links: Garli Mkv implementation

See the tutorial in the Manual (PDF) for BayesTraits

Dec. 6 Slides: BIOL848-lec23-Coalescent.pdf
Dec 8: This week we are going to be working through the *BEAST tutorial ( available from
If you want to run beauti on the cluster, you'll need to use the ssh -X option when you login in.
Dec. 6 Slides: BIOL848-lec24-MSA.pdf