phylogenetic methods 2017

The syllabus is at http://phylo.bio.ku.edu/BIOL848/Syllabus.pdf

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.

Slides

.

Date Link
Aug 21 - Aug 25 http://phylo.bio.ku.edu/BIOL848/lec1-IntroStats.pdf
Aug 25 + Aug 28 http://phylo.bio.ku.edu/BIOL848/lec4-ML-CompatPars.pdf
lec3-skipped-ML-notes.pdf
lec4-ML-Hennig-Compat-notes.pdf
Sep 1 http://phylo.bio.ku.edu/mephytis/barcharts.html
Lab 1: http://phylo.bio.ku.edu/slides/BIOL848-lab1-UnixIntro.html
Sep 6 http://phylo.bio.ku.edu/BIOL848/lec-sep-06-2017.pdf (notes on parsimony algorithms).
Sep 8 http://phylo.bio.ku.edu/BIOL848/lab2.html
http://phylo.bio.ku.edu/BIOL848/lec8-Searching.pdf
Sep 13 hw2.txt
lec9-Distances.pdf
Sep 15 http://phylo.bio.ku.edu/BIOL848/lab3.html
Sep 18 http://phylo.bio.ku.edu/BIOL848/f81-mle.pdf
Sep 22 hw3.txt
Paul Lewis's ML in phylogenetics lecture.
Dave Swofford's Woods Hole lecture on model selection: http://phylo.bio.ku.edu/slides/swofford_WH2017_modsel.pdf
The primate-mtdna.nex.zip data file for the lab.
Dave's lab on model selection with PAUP
Sep 25 http://phylo.bio.ku.edu/BIOL848/lec10-13-models.pdf
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:
https://molevol.mbl.edu/index.php/SnakeTopoParametricBootstrappingLab
and https://molevol.mbl.edu/index.php/CharacterEvoParametricBootstrappingLab
Oct. 9+11 Models (Mkv, covarion, auto-correlated gamma, threshold)
Oct. 13 BIOL848-BayesIntro.pdf
BIOL848-BayesSecond.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 Archery_model.zip 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 http://phylo.bio.ku.edu/content/phylogenetic-methods-2013 for the last version of the course.