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.