phylogenetic methods 2013
Note: Note that the current version of the course is at "https://phylo.bio.ku.edu/courses/phylomethods
This course covers state-of-the-art methods for reconstructing phylogenies. We will cover the theoretical basis for different phylogenetic analyses and learn how to use some of the software packages available for conducting these analyses. Inferences that rely heavily on phylogenetic trees ( eg. analyses of character evolution, divergence time estimation, and studies of diversification rates) will also be covered.
The syllabus is available as a pdf from this link .
I will post pdfs here throughout the semester. I will post the source code for my own notes and some slides to a GitHub repository , but much of the lecture is presented on the board. Bear in mind, that a great deal of the content will be given on the board, and my typed notes may be minimal for those sections of the lectures - make sure that you take good notes!
Some links
Felsenstein's Inferring Phylogenies book is highly recommended for the course.
His list of phylogeny programs is also very helpful.
The website for the Workshops on Molecular Evolution is a good source of lecture slides, software tutorials, and general information.
Slides
| Date | Link |
|---|---|
| Jan 23 | lec1-IntroStats.pdf |
| Jan 25 | lec2-tree-terms.pdf and Homework 2 (due on Wed) |
| Jan 28 | lec3-ParalogyAndInference.pdf |
| Jan 30 | lec4-Inference.pdf |
| Feb 1 | lab 1 Unix terminal and BIOL848-lec5-StatInference-Notes.pdf |
| Feb 4 | lec6-ML-CompatModel-Notes.pdf |
| Feb 6 | lec6-ML-MPModel-Notes.pdf and lec6-ML-MPModelAlgorithms.pdf |
| Feb 8 | lab 2-PaupMesquiteNEXUS |
| Feb 18 | Paul Lewis' parsimony slides are at POL-ParsSlides.pdf and BIOL848-lec8-Searching.pdf |
| Feb 25 | parsSummaryModels.pdf |
| Feb 27 | BIOL848-lec11ML.pdf |
| Mar 1 | lab 3 and lab 4 |
| Mar 4 | treeLikeRateHetIntro.pdf and Homework 3 |
| Mar 6 | BIOL848-rateHetContinued.pdf |
| Mar 8 |
lab 5 (same as last week's lab 4)
and
a GARLI lab
basicNucleotideGarli.txt constrainedNucleotideGarli.txt |