22115 c22115 https://teaching.healthtech.dtu.dk/22115/index.php/22115_-_Computational_Molecular_Evolution MediaWiki 1.41.0 first-letter Media Special Talk User User talk 22115 22115 talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk 0 7 205 204 2026-03-17T21:36:21Z Gorm 3 /* Week 7 (March 18): Bayesian inference of phylogeny */ 205 wikitext text/x-wiki ; Overview [[File:Darwin logo2 medium.png |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/graduate/msc-programmes/bioinformatics MSc in Bioinformatics and Systems Biology] at the [https://www.dtu.dk/english Technical University of Denmark]. The course is taught by Professor Anders Gorm Pedersen, [https://www.healthtech.dtu.dk/english/Research/Research-Sections/Section-Bioinformatics Section for Bioinformatics], [https://www.healthtech.dtu.dk/english 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. __TOC__ =='''Computer setup'''== ===MacOS=== :* [[MacOS software installation]] <!-- :* [[Notes on using MacOS for exercises]] '''UNDER CONSTRUCTION''' --> ===Windows=== :* [[Windows software installation]] <!-- :* [[Windows software installation - Old Version]] --> ===Linux=== :* [[Linux software installation]] <!-- :* [[Notes on using Linux for exercises]] '''UNDER CONSTRUCTION''' --> == '''Lecture Schedule''' == :([[27615 Previous course programs|Course programs, previous years]]) ===Week 1 (February 4): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation=== :; Online lectures :* [https://youtu.be/okjVaLA5S38 Common descent (11:52)] :* [https://youtu.be/VkkIu1ZtaIE Natural selection (14:57)] :* [https://youtu.be/wqa6W3_WW7s Evidence for evolution (part 1) (9:34)] :* [http://y2u.be/_-a-F8egAis Evidence for evolution (part 2) (20:54)] :* [http://y2u.be/AUGbSMWPILE Population growth and selection (18:13)] :; Course material :* [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 :* [[Population Growth, Fitness, and Selection]] ---- ===Week 2 (February 11): Neutral mutations and genetic drift. Tree reconstruction by parsimony=== :; Online lectures :* [https://youtu.be/cQVjL50kK0k Neutral Theory of Molecular Evolution (11:28)] :* [https://youtu.be/J8LDUFm4ttA Genetic Drift (9:35)] :* [https://youtu.be/AZkHWdl2oAw Trees: Terminology and Representation (9:41)] :* [https://youtu.be/zCj1s9fmaKs Homology and Homoplasy (9:07)] :* [https://youtu.be/gXb_WuLCD8g Maximum Parsimony (7:48)] :* [https://youtu.be/Q7ZpdPCx0uQ The Fitch Algorithm (10:31)] :* [https://youtu.be/deywW9wJXmw Searching Tree Space (14:01)] :; 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 :* [[Phylogenetic Analysis using Parsimony]] ---- ===Week 3 (February 18): Consensus trees. Distance matrix methods=== :; Online lectures :* [https://www.youtube.com/watch?v=YXZZyu9OAcg Consensus Trees (16:27)] :* [https://www.youtube.com/watch?v=MhjSSxcGjaY Distance Matrix Methods, part 1 (6:07)] :* [https://www.youtube.com/watch?v=PNoUcQTCxiM Distance Matrix Methods, part 2 (22:28)] :* [https://www.youtube.com/watch?v=Dj24mCLQYUE Neighbour Joining (15:28)] :; 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 :* [[Consensus Trees]] :* [[Distance Matrix Methods]] ---- ===Week 4+5 (February 25 + March 4): Mini project 1=== <!-- 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. 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: * [https://teaching.healthtech.dtu.dk/material/22115/Treequiz1_answers.pdf Tree quiz with answers] --> ---- ===Week 6 (March 11): Models of sequence evolution. Likelihood methods=== :; Online lectures :* [https://youtu.be/ro2MFmVZypQ Models of evolution (28:48)] :* [https://youtu.be/xDKUIegYpWM Maximum likelihood (22:06)] :* [https://youtu.be/Siau2o_egGI Ancestral reconstruction (10:45)] :; Course material :* [[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 :* [[Models of Evolution]] :* [[Maximum Likelihood]] ---- ===Week 7 (March 18): Bayesian inference of phylogeny=== :; Online lectures :* [https://www.youtube.com/watch?v=DI3TIx78NqM&t=12s Bayesian Inference (23:48)] :* [https://youtu.be/uyG5DVigEyM?list=PLXwjzs_mabFrlRF7uALEomfGGckG0sG5y Markov chain Monte Carlo (19:54)] :; 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] :* [[Media: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?"] :* [https://gwern.net/doc/statistics/bayes/2003-brooks.pdf Background reading: "Bayesian computation: a statistical revolution"] :; Computer exercise :* [[Bayesian Phylogeny]] ---- ===Week 8+9 (March 25 + April 8): Mini project 2=== <!-- '''Maximum likelihood and R-based phylogenetics - The origin of the Lassa and SARS-CoV-2 virus epidemics''' '''Project description and data sets''': See DTU Learn page The mini project should be submitted and assessed via the peergrade interface at DTU Learn. --> ---- ===Week 10 (April 15): Model Selection=== :; Online lectures :* [https://youtu.be/sJB2LmppZj8?list=PLXwjzs_mabFrlRF7uALEomfGGckG0sG5y Model selection, part 1 (15:19)] :* [https://youtu.be/qSoDZ_33GbM Model selection, part 2 (17:20)] :* [https://youtu.be/YYoo1vUO4ME Introduction to computer exercise: detection of selection (15:24)] :; 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] :; Computer exercise :* [[Model selection]] ---- ===Week 11 (April 22): Bayesian Phylogenetics, Part 2 === :; 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://beast.community/analysing_beast_output Analysing BEAST output using Tracer] :* [https://beast.community/tracer_convergence Identifying convergence problems using Tracer] :* [https://taming-the-beast.org/tutorials/Troubleshooting-initialization-issues/ Troubleshooting initialization issues] :* [https://taming-the-beast.org/tutorials/Troubleshooting-convergence-issues/ Troubleshooting convergence issues] :; Computer exercise :* [[Bayesian phylogenetics: checking convergence]] :* [[Bayesian phylogenetics: clock models]] ---- ===Week 12 + 13 (April 20 + May 6): Mini project 3: Final exam=== '''Details will follow''' ---- cjwwnpo913zqkmslb6rlgtwy29gptf4