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
Jan 23 lec1-IntroStats.pdf
Jan 25 lec2-tree-terms.pdf and Homework 2 (due on Wed)
Jan 28 lec3-ParalogyAndInference.pdf
Jan 30 lec4-Inference.pdf
Feb 1 lab 1 Unix terminal and BIOL848-lec5-StatInference-Notes.pdf
Feb 4 lec6-ML-CompatModel-Notes.pdf
Feb 6 lec6-ML-MPModel-Notes.pdf and lec6-ML-MPModelAlgorithms.pdf
Feb 8 lab 2-PaupMesquiteNEXUS
Feb 18 Paul Lewis' parsimony slides are at POL-ParsSlides.pdf and BIOL848-lec8-Searching.pdf
Feb 25 parsSummaryModels.pdf
Feb 27 BIOL848-lec11ML.pdf
Mar 1 lab 3 and lab 4
Mar 4 treeLikeRateHetIntro.pdf and Homework 3
Mar 6 BIOL848-rateHetContinued.pdf
Mar 8 lab 5 (same as last week's lab 4) and a GARLI lab


Mar 11 HolderTestingLectureWoodsHole2012.pdf
Mar 15 Parametric Bootstrapping Lab for Windows which requires the CygWin DLL from cygwin be in the same directory as the executable.
Week of Mar 25 BIOL848-BayesIntro.pdf


Recommended Lab: Jeremy Brown's MrBayes lab
Alternate Labs: Woods Hole labs
Holder/Lewis old MrBayes Lab. The algaemb datafile is here.
The jc.nex datafile is here.
The mac executable is here. An old version is here
Apr 1 lec18-BayesFactors.pdf
Apr 3, 8 lec19-AncStates.pdf (corrected Apr 5)
Apr 5 See Jeremy Brown's MrBayes lab Some background on the MrBayes labs from woods hole: MrBayes_tutorial.txt
Apr 10 lec20-CharEvol.pdf
Apr 11 Your choice of a Mesquite lab on character state estimation
or you can try out GARLI's impmentation of the Mk model, or
See the tutorial in the Manual (PDF) for BayesTraits
Apr 10-17 lec22-MorphologicalCharacters.pdf
Tracy Heath's div times slides
Apr 19 Tracy Heath's BEAST lab and (mainly Joe Felsenstein's) slides on the coalescent lec23-Coalescent.pdf
Apr 10-17 I'll use some slides from Joseph Heled's Feb 2013 talk in Austin
Apr 26 I'll use some slides from Joseph Heled's *BEAST tutorial
Apr 29 lec24-MSA.pdf, and I'll use some slides from Joe Bielawski's lecture on codon models from Joe's site
May 3 lab. Check out either the RAxML lab at

or the Joe Bielawski's PAML lab posted at