2014 SISG Module 12

Molecular Phylogenetics

Instructors:

Mark Holder
Jeffrey Thorne
Joe Felsenstein


Course syllabus


Lecture slides:

These are not yet 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)
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 will become active as each lecture's audio files are posted.

WMA formatMP3 format
Introduction, parsimony, distance (Mark Holder) Lecture1.WMA Lecture1.mp3
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) Lab2.WMA Lab2.mp3
More likelihood and bootstraps (Joe Felsenstein) Lecture5.WMA Lecture5.mp3
More realistic models (Jeff Thorne) Lecture6.WMA Lecture6.mp3
Bayesian inference (Jeff Thorne) Lecture7.WMA Lecture7.mp3
MrBayes lab (Mark Holder) Lab3a.WMA
Lab3b.WMA
Lab3a.mp3
Lab3b.mp3
Tutorial (all three) Tutorial.WMA Tutorial.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 


Lecture handouts:

These are PDFs of the lecture slides, in 2-up layout and noncolor format, as submitted to SISG so that they can produce the printed version that students are issued. They are very similar to the lecture slides that are available above, except for format and color, and the absence of some of the animated effects.

Introduction, parsimony, distance (Mark Holder)
Topology searching (Mark Holder)
PAUP* lab (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)
Divergence times (Jeff Thorne)
BEAST demo materials (Mark Holder)
Comparative methods, the coalescent, and the future (Joe Felsenstein)


Programs:

Here you will find information on the new PHYLIP programs which we will be making available on a test basis.

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


Data sets:

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