mtholder.github.io/home/

The syllabus is at "https://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	"https://phylo.bio.ku.edu/BIOL848/lec1-IntroStats.pdf
Aug 25 + Aug 28	"https://phylo.bio.ku.edu/BIOL848/lec4-ML-CompatPars.pdf lec3-skipped-ML-notes.pdf lec4-ML-Hennig-Compat-notes.pdf
Sep 1	"https://phylo.bio.ku.edu/mephytis/barcharts.html Lab 1: "https://phylo.bio.ku.edu/slides/BIOL848-lab1-UnixIntro.html
Sep 6	"https://phylo.bio.ku.edu/BIOL848/lec-sep-06-2017.pdf (notes on parsimony algorithms).
Sep 8	"https://phylo.bio.ku.edu/BIOL848/lab2.html "https://phylo.bio.ku.edu/BIOL848/lec8-Searching.pdf
Sep 13	hw2.txt lec9-Distances.pdf
Sep 15	"https://phylo.bio.ku.edu/BIOL848/lab3.html
Sep 18	"https://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: "https://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	"https://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 "https://phylo.bio.ku.edu/content/phylogenetic-methods-2013 for the last version of the course.