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(UConn EEB 396-014)

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PhyloMath is an experimental course being offered Spring 2004 under the course number 396 ("Investigation of Special Topics"). Although some of the material offered in PhyloMath will be incorporated into my Phylogenetics course (to be offered for the first time Spring 2005), the goals for the two courses are somewhat different. Phylogenetics will strive to present a well-rounded introduction to phylogeny reconstruction and applications of phylogenetics in ecology, evolution and systematics. PhyloMath attempts to cover the nitty-gritty details of model-based phylogenetics, and thus assumes that the student already has considerable experience with phylogeny estimation and wants to develop a much more thorough understanding of how the model-based methods work. The PhyloMath course does not assume that you remember your 8th grade algebra or your first semester of undergraduate calculus, but you should be prepared to put some time into these subjects if you are rusty.

I am experimenting with a new means of student participation this semester (which I learned about from Tanya Berger-Wolf). Students taking the course for credit are expected to sign up to prepare notes for one of the lectures. This has two advantages: 1) it makes the student aware of just how much (or little) they understood from the lecture; and 2) it makes me aware of just how much (or little) the students are understanding from the lecture! This allows me to correct my course if I start assuming too much background knowledge on the part of the participants. I predict this system will work really well. If you are a current student in the course reading this, I might add that I think you will get the most out of this course if you actually prepare notes for every lecture, not just the one for which you have signed up.

PhyloMath courses elsewhere

Copyright notice

All lecture notes (PDF files) linked to this site are copyright 2004 by the author of the document. Visitors are welcome to browse, but please do not use these documents as sources for other publications without first contacting the author.


The class meets Tuesdays 12-2pm in Torrey Life Science room 179 (starting Feb. 10). Sitters-in are welcome.

Date Notes Preparer Topics Link to PDF
January 20, 2004 Paul O. Lewis Simulation of one sequence, likelihood of one sequence under JC and F81 models, logarithms Paul's notes
January 27, 2004 NO CLASS - Paul convalescing
February 3, 2004 Jon Richmond Simulation of two sequences, likelihood of two sequences under JC model, time reversibility, binomial "straw man" model Jon's notes
February 10, 2004 Norm Wickett Expected values, binomial to poisson, transition equations, joint and conditional probabilities Norm's notes
February 17, 2004 Brigid O'Donnell Expected number of substitutions, PDFs, CDFs, derivatives, integrals, sojourn times Brigid's notes
February 24, 2004 Jessica Budke Sojourn times, estimating JC distances, Method of Moments, Method of Maximum Likelihood, rate heterogeneity, proportion of invariable sites Jessica's notes
March 2, 2004 Roberta Engel Gamma distributed relative rates Roberta's notes
March 9, 2004 NO CLASS - Spring Break
March 16, 2004 Maxi Polihronakis Other substitution models: K2P, HKY, F84, GTR, amino acid models Maxi's notes
March 23, 2004 Dan Vanderpool, Andreas Bernauer Transition:transversion ratio vs. rate ratio, site likelihoods of a 4-taxon tree Lecture 8: Dan's notes,
Andreas' notes,
Paul's handout
March 30, 2004 Carrie Fyler Likelihood with rate heterogeneity, molecular clock constraint, introduction to Bayesian inference Carrie's notes
April 6, 2004 Michael McAloon Bayesian inference (cont.), phylogenetic Markov chain Monte Carlo Michael's notes, BayesianDist.xls (warning: xls file is now up to 6.6 megabytes!)
April 13, 2004 Hilary McManus MCMC continued, plus intro to codon models Hilary's notes, Codon model rate matrix
April 15, 2004 Jeff Thorne visits and gives EEB Seminar
April 20, 2004 Jadranka Rota MCMC continued: Hastings ratio, LOCAL move, sliding windows, etc. Jadranka's notes
April 27, 2004 Nic Tippery Bayes' factors, discrete morphology model, ...

Instructor Contact Information

Paul O. Lewis, Instructor
Assistant Professor of Ecology and Evolutionary Biology
Office: Torrey Life Science Room 166a
Telephone: (860) 486-2069