22115 - Computational Molecular Evolution: Difference between revisions
Jump to navigation
Jump to search
(Created page with "; Overview right|border|550px : This page contains links to video lectures, computer exercises, and other material for the course [https://kurser.dtu.dk/course/22115 22115 - Computational Molecular Evolution], which is part of the [https://www.dtu.dk/english/education/msc/programmes/systems_biology MSc in Bioinformatics and Systems Biology] at the [https://www.dtu.dk/english Technical University of Denmark]. The course is taught by Prof...") |
|||
| Line 45: | Line 45: | ||
:; Course material | :; Course material | ||
:* [https://github.com/agormp/evolintro/blob/main/evolintro.pdf Lecture notes on evolutionary theory and population genetics] | :* [https://github.com/agormp/evolintro/blob/main/evolintro.pdf Lecture notes on evolutionary theory and population genetics] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/slides_week1.pdf Slides, week 1] | ||
:; Computer exercise | :; Computer exercise | ||
| Line 64: | Line 64: | ||
:; Course material | :; Course material | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/slides_week2.pdf Slides, week 2] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/Paup_Doc_31.pdf PAUP 3.1 manual (note: for older version - contains explanations of parsimony and tree moves)] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/PAUP4-manual.pdf PAUP 4beta command reference] | ||
:; Computer exercise | :; Computer exercise | ||
| Line 93: | Line 93: | ||
===Week 4+5 (February 21 + 28): Mini project 1=== | ===Week 4+5 (February 21 + 28): Mini project 1=== | ||
< | <#-- | ||
Project description: [[Media:Miniproject1 whales.pdf|Building a tree from scratch: What are the closest relatives of whales?]] | Project description: [[Media:Miniproject1 whales.pdf|Building a tree from scratch: What are the closest relatives of whales?]] | ||
| Line 119: | Line 119: | ||
:* [[Media:Handout likelihood.pdf|Handout exercise: Computation of Likelihood]] | :* [[Media:Handout likelihood.pdf|Handout exercise: Computation of Likelihood]] | ||
:* [[Media:Slides week4.pdf|Slides, week 6]] | :* [[Media:Slides week4.pdf|Slides, week 6]] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/substitutionmodels.pdf Lecture notes: Substitution models] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/main.pdf Optional lecture notes: Matrix exponentials for Markov chains] | ||
:; Computer exercises | :; Computer exercises | ||
:* [[Models of Evolution]] | :* [[Models of Evolution]] | ||
Revision as of 14:22, 19 March 2024
- Overview
- This page contains links to video lectures, computer exercises, and other material for the course 22115 - Computational Molecular Evolution, which is part of the MSc in Bioinformatics and Systems Biology at the Technical University of Denmark. The course is taught by Professor Anders Gorm Pedersen, Section for Bioinformatics, Department of Health Technology.
- The main goal of this course is to give an introduction to theory and algorithms in the field of computational molecular evolution. We will cover basic evolutionary theory (common descent, natural selection, genetic drift, models of growth and selection), and the main types of algorithms used for constructing and analyzing phylogenetic trees (parsimony, distance based methods, maximum likelihood methods, and Bayesian inference). We will also discuss the role of statistical modeling in science more generally
- The course will consist of lectures, computer exercises, and mini-projects. The student will acquire practical experience in the use of a range of computational methods by analyzing sequences from the scientific literature.
Computer setup
Linux
Windows
MacOS
Lecture Schedule
Week 1 (January 31): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation
- Online lectures
- Computer exercise
Week 2 (February 7): Neutral mutations and genetic drift. Tree reconstruction by parsimony
- Online lectures
- Course material
- Computer exercise
Week 3 (February 14): Consensus trees. Distance matrix methods
- Online lectures
- Course material
- Computer exercises
Week 4+5 (February 21 + 28): Mini project 1
<#--
Project description: Building a tree from scratch: What are the closest relatives of whales?
The mini project should be submitted and assessed via a peer assessment module that will become available on the course DTU Learn page.
Take this tree quiz to test yourself on your ability to accurately interpret evolutionary trees:
Check your replies here:
-->
Week 6 (March 6): Models of sequence evolution. Likelihood methods
- Online lectures
- Course material
- Handout exercise: Real, Observed, and Expected Change
- Handout exercise: Computation of Likelihood
- Slides, week 6
- Lecture notes: Substitution models
- Optional lecture notes: Matrix exponentials for Markov chains
- Computer exercises
Week 7 (March 13): Bayesian inference of phylogeny
- Online lectures
- Course material
- Computer exercise
Week 8+9 (March 20 + April 3): Mini project 2
Week 10 (April 10): Model Selection
- Online lectures
- Course material
- Computer exercise
Week 11 (April 17): Bayesian Phylogenetics, Part 2
- Course material
Week 12 + 13 (April 24 + May 1): Mini project 3: Final exam
Details will follow