phylogenetic methods 2017

The syllabus is at

We will use the Blackboard site for copyrighted material that cannot be distributed.

The website for the Workshops on Molecular Evolution is a good source of lecture slides, software tutorials, and general information.


Date Link
Aug 21 - Aug 25
Aug 25 + Aug 28
Sep 1
Lab 1:
Sep 6 (notes on parsimony algorithms).
Sep 8
Sep 13 hw2.txt
Sep 15
Sep 18
Sep 22 hw3.txt
Paul Lewis's ML in phylogenetics lecture.
Dave Swofford's Woods Hole lecture on model selection:
The data file for the lab.
Dave's lab on model selection with PAUP
Sep 25
Sep 29 Emily Jane McTavish's ML Searching Lab
Oct. 2+4 testing phylogenetic hypotheses
Studying phylomethod performance with simulations
Oct 6 Parametric bootstrapping labs:
Oct. 9+11 Models (Mkv, covarion, auto-correlated gamma, threshold)
Oct. 13 BIOL848-BayesIntro.pdf
Paul Lewis' MCMCRobot

See for the last version of the course.