22115 - Computational Molecular Evolution: Difference between revisions
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(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...") |
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:([[27615 Previous course programs|Course programs, previous years]]) | :([[27615 Previous course programs|Course programs, previous years]]) | ||
===Week 1 ( | ===Week 1 (February 5): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation=== | ||
:; Online lectures | :; Online lectures | ||
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:; 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 | ||
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===Week 2 (February | ===Week 2 (February 12): Neutral mutations and genetic drift. Tree reconstruction by parsimony=== | ||
:; Online lectures | :; Online lectures | ||
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:; 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 | ||
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===Week 3 (February | ===Week 3 (February 19): Consensus trees. Distance matrix methods=== | ||
:; Online lectures | :; Online lectures | ||
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:; Course material | :; Course material | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/Consensus.pdf Handout exercise: Consensus Trees] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/Distance_handout.pdf Handout exercise: Distance Matrix Methods] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/Slides_week3.pdf Slides, week 3] | ||
:; Computer exercises | :; Computer exercises | ||
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===Week 4+5 (February | ===Week 4+5 (February 26 + March 5): Mini project 1=== | ||
<!-- | <!-- | ||
Project description: [ | Project description: [https://teaching.healthtech.dtu.dk/material/22115/Miniproject1_whales.pdf 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. | 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: | Take this tree quiz to test yourself on your ability to accurately interpret evolutionary trees: | ||
* [ | * [https://teaching.healthtech.dtu.dk/material/22115/Treequiz1.pdf Tree quiz] | ||
Check your replies here: | Check your replies here: | ||
* [ | * [https://teaching.healthtech.dtu.dk/material/22115/Treequiz1_answers.pdf Tree quiz with answers] | ||
--> | --> | ||
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===Week 6 (March | ===Week 6 (March 12): Models of sequence evolution. Likelihood methods=== | ||
:; Online lectures | :; Online lectures | ||
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:; Course material | :; Course material | ||
:* [[Media: | :* [[Media: Expectedchange.pdf | Handout exercise: Real, Observed, and Expected Change]] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/Handout_likelihood.pdf Handout exercise: Computation of Likelihood] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/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]] | ||
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===Week 7 (March | ===Week 7 (March 19): Bayesian inference of phylogeny=== | ||
:; Online lectures | :; Online lectures | ||
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:; Course material | :; Course material | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/Handout.class08.pdf Handout exercise: Bayesian estimation of model parameter value] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/Slides_week5.pdf Slides, week 7] | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/MTN122.pdf| An Introduction to Bayesian Statistics Without Using Equations] | ||
:* [http://www.nature.com/nbt/journal/v22/n9/pdf/nbt0904-1177.pdf Background reading: "What is Bayesian statistics?"] | :* [http://www.nature.com/nbt/journal/v22/n9/pdf/nbt0904-1177.pdf Background reading: "What is Bayesian statistics?"] | ||
:* [http://rsta.royalsocietypublishing.org/content/roypta/361/1813/2681.full.pdf Background reading: "Bayesian computation: a statistical revolution"] | :* [http://rsta.royalsocietypublishing.org/content/roypta/361/1813/2681.full.pdf Background reading: "Bayesian computation: a statistical revolution"] | ||
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===Week 8+9 (March | ===Week 8+9 (March 26 + April 2): Mini project 2=== | ||
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===Week 10 (April | ===Week 10 (April 9): Model Selection=== | ||
:; Online lectures | :; Online lectures | ||
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:; Course material | :; Course material | ||
:* [ | :* [https://teaching.healthtech.dtu.dk/material/22115/Slides_week6.pdf Slides, week 10] | ||
:* [https://github.com/ddarriba/jmodeltest2/files/157130/manual.pdf jmodeltest manual] | :* [https://github.com/ddarriba/jmodeltest2/files/157130/manual.pdf jmodeltest manual] | ||
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===Week 11 (April | ===Week 11 (April 23): Bayesian Phylogenetics, Part 2 === | ||
:; Course material | :; Course material | ||
:* [https://www.researchgate.net/publication/319965471_A_biologist%27s_guide_to_Bayesian_phylogenetic_analysis A biologist’s guide to Bayesian phylogenetic analysis] | :* [https://www.researchgate.net/publication/319965471_A_biologist%27s_guide_to_Bayesian_phylogenetic_analysis A biologist’s guide to Bayesian phylogenetic analysis] | ||
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===Week 12 + 13 (April | ===Week 12 + 13 (April 30 + May 7): Mini project 3: Final exam=== | ||
'''Details will follow''' | '''Details will follow''' | ||
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Latest revision as of 17:39, 11 March 2025
- 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 (February 5): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation
- Online lectures
- Computer exercise
Week 2 (February 12): Neutral mutations and genetic drift. Tree reconstruction by parsimony
- Online lectures
- Course material
- Computer exercise
Week 3 (February 19): Consensus trees. Distance matrix methods
- Online lectures
- Course material
- Computer exercises
Week 4+5 (February 26 + March 5): Mini project 1
Week 6 (March 12): 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 19): Bayesian inference of phylogeny
- Online lectures
- Course material
- Computer exercise
Week 8+9 (March 26 + April 2): Mini project 2
Week 10 (April 9): Model Selection
- Online lectures
- Course material
- Computer exercise
Week 11 (April 23): Bayesian Phylogenetics, Part 2
- Course material
Week 12 + 13 (April 30 + May 7): Mini project 3: Final exam
Details will follow