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19 March 2024
- 15:0015:00, 19 March 2024 diff hist +545 22115 - Computational Molecular Evolution No edit summary
- 14:4814:48, 19 March 2024 diff hist +3,101 N Bayesian phylogenetics: clock models Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Overview == In this exercise we will explore how to use the software tool BEAST2 to construct phylogenies based on molecular-clock models. In previous exercises we have worked with phylogenies where we did not have information about how fast sequences were evolving, and we therefore used the number of substitutions as branch lengths. When the..."
- 14:4714:47, 19 March 2024 diff hist 0 N File:Tracer ugly caterpillar.png No edit summary current
- 14:4614:46, 19 March 2024 diff hist 0 N File:Tracer hairy caterpillar.png No edit summary current
- 14:4514:45, 19 March 2024 diff hist 0 N File:Tracer lousy convergence.png No edit summary current
- 14:4514:45, 19 March 2024 diff hist 0 N File:Tracer marginals overlap.png No edit summary current
- 14:4414:44, 19 March 2024 diff hist 0 N File:Tracer fileload2.png No edit summary current
- 14:4414:44, 19 March 2024 diff hist +5,071 N Bayesian phylogenetics: checking convergence Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Check convergence using Tracer == In this exercise you will be briefly introduced to how to check if an MCMC run has converged using the program Tracer from the BEAST2 package. You will do this by re-examining the output from the Bayesian analysis you did in the week 9 exercise. ---- '''Question 1''' : Issue this command to start the Trace..." current
- 14:4314:43, 19 March 2024 diff hist −3 Model selection →Analysis of viral data set: alignment of coding DNA
- 14:4314:43, 19 March 2024 diff hist 0 N File:Molevol-Downloads-aictable.png No edit summary current
- 14:4214:42, 19 March 2024 diff hist +23,528 N Model selection Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Overview == : In this exercise you are going to investigate features of HIV-1 evolution. You will do this by analyzing a large set of env-genes from HIV-1, subtype B. specifically, the DNA sequences analyzed here correspond to a region surrounding the hypervariable V3 region of the gp120 protein. : Like other retroviruses, particles of HIV..."
- 14:4114:41, 19 March 2024 diff hist +26,633 N Bayesian Phylogeny Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Overview == Today's exercise will focus on phylogenetic analysis using Bayesian methods. As was the case for likelihood methods, Bayesian analysis is founded on having a probabilistic model of how the observed data is produced. (This means that, for a given set of parameter values, you can compute the probability of any possible data set)...." current
- 14:3914:39, 19 March 2024 diff hist +5,361 N Maximum Likelihood Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Overview == The data set you will work with here consists of an alignment of full length mitochondrial DNA from human (53 sequences), chimpanzee (1 sequence), bonobo (1 sequence), and Neanderthal (1 sequence). The Neanderthal DNA was extracted from archaeological material, specifically 38,000 year old bones found at Vindija in Croatia (all s..."
- 14:3514:35, 19 March 2024 diff hist +20,813 N Models of Evolution Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Overview == In this exercise we will explore a number of different, but closely related, models of evolution. Using such models it is possible to estimate the number of unseen mutational events and thereby obtain genetic distances that have been corrected for superimposed substitutions. It is, however, important to realize that these correct..." current
- 14:3414:34, 19 March 2024 diff hist −3 Distance Matrix Methods →Getting started current
- 14:3114:31, 19 March 2024 diff hist +13,863 N Distance Matrix Methods Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Getting started == : '''Note:''' If you didn't already do this during the video lecture: Start by doing the [https://teaching.healthtech.dtu.dk/22115/images/3/3f/Distance_handout.pdf handout exercise for distance matrix methods]. : In this exercise we will reconstruct phylogenetic trees using a variety of distance-based methods. Specificall..."
- 14:2714:27, 19 March 2024 diff hist 0 N File:Figtreenext.png No edit summary current
- 14:2614:26, 19 March 2024 diff hist +7,322 N Consensus Trees Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Getting started == '''1: Start Terminal window''' '''2: Construct working directory:''' : In the command below: Instead of <code>/path/to/molevol</code> enter the path to the directory where you have placed your course files (for instance <code>cd /Users/bob/Documents/molevol</code>, or <code>cd /home/student/molevol</code>). cd /path/to/m..." current
- 14:2514:25, 19 March 2024 diff hist +21,556 N Phylogenetic Analysis using Parsimony Created page with "This exercise is part of the course Computational Molecular Evolution (22115). == Overview == In this exercise you are going to examine three different data sets using the PAUP* program. All analyses will be performed under the parsimony criterion. Data set 1 consists of genomic nucleotide sequences from 9 primate species. This set is sufficiently small that an exhaustive search of all possible trees can be performed. Dat..." current
- 14:2314:23, 19 March 2024 diff hist +21,331 N Population Growth, Fitness, and Selection Created page with "This exercise is part of the course Computational Molecular Evolution (22115). === Overview === In this exercise you are going to use a simple computer program for simulating the growth of a population. The simulation will be based on an exponential growth model and will involve organisms having one of two different genotypes ('A' and 'a'). By performing the simulation with a range of different model parameter values you w..." current
- 14:2214:22, 19 March 2024 diff hist −2 22115 - Computational Molecular Evolution →Lecture Schedule
- 14:1714:17, 19 March 2024 diff hist +11,269 N Computational Molecular Evolution 22115 - 2021 Created page with "; Overview right|border|450px : 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,..." current
- 14:1614:16, 19 March 2024 diff hist +8,014 N Computational Molecular Evolution 22115 - 2020 Created page with " ===Week 1 (February 5): 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 (..." current
- 14:1514:15, 19 March 2024 diff hist +6,402 N Molecular Evolution 27615 - 2016 Created page with "== '''Lecture Schedule 2016''' == ===Week 1 (February 3): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation=== :; Online lectures :* [https://class.coursera.org/molevol-003/lecture/11 Common descent (11:52)] :* [https://class.coursera.org/molevol-003/lecture/15 Natural selection (14:57)] :* [https://class.coursera.org/molevol-003/lecture/17 Evidence for evolution (part 1) (9:34)] :* [https://class.coursera.org/molevo..." current
- 14:1514:15, 19 March 2024 diff hist +144 N 27615 Previous course programs Created page with "* Molecular Evolution 27615 - 2016 * Computational Molecular Evolution 22115 - 2020 * Computational Molecular Evolution 22115 - 2021" current
- 14:1414:14, 19 March 2024 diff hist +3 Linux software installation No edit summary current
- 14:1314:13, 19 March 2024 diff hist +2 MacOS software installation No edit summary current
- 14:1214:12, 19 March 2024 diff hist +5,008 N MacOS software installation Created page with "These are instructions for how to install software and data used on the course Computational Molecular Evolution (22115) when using the MacOS operating system. == Check which shell you are using, and specify .rc file == Depending on what version of MacOS you are using, [https://support.apple.com/en-us/HT208050 your shell is probably either bash or zsh]. This plays a role when you want to set [https://en.wikipedia.org/wiki/E..."
- 14:1014:10, 19 March 2024 diff hist +4,883 N Windows software installation Created page with "These are instructions for how to install software and data used on the course Computational Molecular Evolution (22115) when using the Windows operating system. __TOC__ == Windows 10 == Installing and running Windows Subsystem for Linux 2 (WSL2) is simpler on Windows 11. We therefore recommend that you [https://www.microsoft.com/en-us/windows/windows-11-specifications upgrade to Windows 11 if possible]. If you can't upgrad..." current
- 14:0814:08, 19 March 2024 diff hist −4 Linux software installation No edit summary
- 14:0814:08, 19 March 2024 diff hist −8 Linux software installation No edit summary
- 14:0714:07, 19 March 2024 diff hist 0 Linux software installation No edit summary
- 14:0414:04, 19 March 2024 diff hist +4,503 N Linux software installation Created page with " These are instructions for how to install software and data used on the course Computational Molecular Evolution (22115) when using the Linux operating system. The commands assume you are using the [https://ubuntu.com/server/docs/package-management apt package manager] used on e.g. Ubuntu Linux. '''Note''': If your computer uses a CPU based on the ARM architecture, rather than the more common Intel or AMD (x86_64) archite..."
- 14:0314:03, 19 March 2024 diff hist 0 N File:Darwin logo2 medium.png No edit summary current
- 13:3613:36, 19 March 2024 diff hist +8,559 N 22115 - Computational Molecular Evolution 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..."
- 13:3513:35, 19 March 2024 diff hist +41 N MediaWiki:Mainpage Created page with "22115 - Computational Molecular Evolution" current
- 13:3313:33, 19 March 2024 diff hist −23 MediaWiki:Sidebar No edit summary current
- 13:3313:33, 19 March 2024 diff hist +155 N MediaWiki:Sidebar Created page with " * navigation ** https://teaching.healthtech.dtu.dk/|Course List ** https://teaching.healthtech.dtu.dk/22115/|Course 22115 ** Programme|Programme * TOOLBOX"
- 13:3213:32, 19 March 2024 diff hist 0 N MediaWiki:Disclaimers Created blank page current
- 13:3113:31, 19 March 2024 diff hist 0 N MediaWiki:Aboutsite Created blank page current
- 13:3113:31, 19 March 2024 diff hist 0 N MediaWiki:Privacy Created blank page current
