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!
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.
|Jan 25||lec2-tree-terms.pdf and Homework 2 (due on Wed)|
|Feb 1||lab 1 Unix terminal and BIOL848-lec5-StatInference-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|
|Mar 1||lab 3 and lab 4|
|Mar 4||treeLikeRateHetIntro.pdf and Homework 3|
|Mar 8|| lab 5 (same as last week's lab 4) and a GARLI lab
|Mar 15||Parametric Bootstrapping Lab
seq-gen.zip 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 3, 8||lec19-AncStates.pdf (corrected Apr 5)|
|Apr 5||See Jeremy Brown's MrBayes lab MrBayes_tutorial.zip Some background on the MrBayes labs from woods hole: MrBayes_tutorial.txt|
|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
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 http://sco.h-its.org/exelixis/hands-On.html
or the Joe Bielawski's PAML lab posted at http://myweb.dal.ca/js551958/PAML_lab/lab.html