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
Oct 20 Jeremy Brown's MrBayes lab . It has links to Tracer and MrBayes in the lab. RWTY is the more recent R-based version of AWTY referred to in the lab.
Oct 23 Tracy Heath's graphical models and Divergence time estimation lectures.
Oct 27 We are going to work through a couple tutorials hosted by the awesome Taming the BEAST workshops . Specifically the introductory tutorial and Tracy Heath's Divergence time tutorial .
Oct 30 Peter Beerli's coalescent slides from Woods Hole 2017
Nov 1 Peter Beerli's coalescent slides part 2 from Woods Hole 2017
Nov 3 RevBayes is available from here . We'll be working through 2 tutorials by Tracy Heath: the non phylogenetic as a general demo, and her RB_TotalEvidenceDating_FBD_Tutorial.pdf tutorial (using this data and these scripts )
Nov 6+8 Laura Kubatko's Species Tree Estimation and Astral + SVDQuartets slides
Nov 10 Laura Kubatko's SVDQuartets and ASTRAL tutorials. Except we'll each need to install Astral. See it's installation instructions
Nov 15 + 20 Stealing slides from Joe Bielawski these lectures to talk about codon models
Nov 27 MSA.pdf
Dec 1 Your choice: Joe Bielawski's PAML lab or Luke Harmon's BiSSE + HiSSE tutorial . Data for Hisse here for grunts.phy and here for grunts.csv

See for the last version of the course.