2016 SISG Module 19

Molecular Phylogenetics


Mark Holder
Jeffrey Thorne
Joe Felsenstein

Course syllabus

Lecture slides:

These have become available. They will be mostly in PDF format (one is in HTML format):

Introduction, parsimony, distance (Mark Holder)
Topology searching (Mark Holder)
PAUP* (Mark Holder)
Nucleotide substitution models etc. (Jeff Thorne)
Likelihood (Joe Felsenstein)
PHYLIP lab materials (Joe Felsenstein)
PAUP* lab materials (Mark Holder)
Bootstraps (Joe Felsenstein)
More realistic models (Jeff Thorne)
Bayesian inference (Jeff Thorne)
MrBayes lab (Mark Holder)
BEAST demo materials (Mark Holder)
Divergence times (Jeff Thorne)
Comparative methods, the coalescent, and the future (Joe Felsenstein)

Lecture audio recordings:

These will each be posted in two formats: WMA and MP3. The links currently do not work; each will become active as that lecture's audio files are posted, on the same day as the lecture.

If you want to hear the corresponding talks from the 2014 course (the most recent time we gave it) look here.

WMA formatMP3 format
Introduction, trees, parsimony (Mark Holder) Lecture1.WMA Lecture1.mp3
Distance methods, topology searching (Mark Holder) Lecture2.WMA Lecture2.mp3
PAUP* Lab (Mark Holder) Lab1.WMA Lab1.mp3
Nucleotide substitution models etc. (Jeff Thorne) Lecture3.WMA Lecture3.mp3
Likelihood (Joe Felsenstein) Lecture4.WMA Lecture4.mp3
PHYLIP Lab (Joe Felsenstein) Lab2a.WMA Lab2a.mp3
PAUP* Lab (Mark Holder) Lab2b.WMA Lab2b.mp3
Bootstraps (Joe Felsenstein) Lecture5.WMA Lecture5.mp3
PHYLIP and PAUP* bootstrap lab (Joe and Mark) Lab2c.WMA Lab2c.mp3
More realistic models (Jeff Thorne) Lecture6.WMA Lecture6.mp3
Tutorial (all three) Tutorial.WMA Tutorial.mp3
Bayesian inference (Jeff Thorne) Lecture7.WMA Lecture7.mp3
MrBayes lab (Mark Holder) Lab3.WMA Lab3.mp3
Divergence times (Jeff Thorne) Lecture8.WMA Lecture8.mp3
BEAST demonstration (Mark Holder) Lab4.WMA Lab4.mp3
The coalescent and comparative method and the future (Joe Felsenstein) Lecture9.WMA  Lecture9.mp3 


We are continually revising the webpages for the programs used in the lab exercises. The main webpage for them is here.


In that webpage you will find information on the new PHYLIP programs which we are making available on a test basis.


For the PAUP* and MrBayes labs, Mark Holder has a web page It has links for PAUP* and for the data sets used in those labs. They are in the Nexus format. When saving those data sets from your browser using the Save As choice in the browser's File menu, make sure they end up with an extension of .nex

Mark has also put nearby Nexus versions of the data sets that Joe collected for his PHYLIP labs. They are here.

MCMC simulations

For learning about MCMC methods, two teaching programs are very helpful:

  1. Paul Lewis's remarkable program MCRobot
  2. For Mac OS X, John Huelsenbeck has a program iMCMC that is inspired by McRobot which will be found at his group's software site here. Scroll down until you see it. The download is a Zip archive, which may require you to reaffirm that this is a legal download and not some wierd virus (it is OK).

R software

I have a web page here that describes using PHYLIP as well as the R packages phangorn and Rphylip which we will use in our labs.

Data sets:

A folder of data sets that can be used in the lab sessions will be found here.