https://teaching.healthtech.dtu.dk/22115/index.php?action=history&feed=atom&title=Molecular_Evolution_27615_-_2016 2026-05-04T18:16:24Z Revision history for this page on the wiki MediaWiki 1.41.0 https://teaching.healthtech.dtu.dk/22115/index.php?title=Molecular_Evolution_27615_-_2016&diff=19&oldid=prev 2024-03-19T13:15:59Z

<p>Created page with &quot;== &#039;&#039;&#039;Lecture Schedule 2016&#039;&#039;&#039; == ===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...&quot;</p> <p><b>New page</b></p><div>== &#039;&#039;&#039;Lecture Schedule 2016&#039;&#039;&#039; ==<br /> <br /> ===Week 1 (February 3): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation===<br /> <br /> :; Online lectures<br /> :* [https://class.coursera.org/molevol-003/lecture/11 Common descent (11:52)]<br /> :* [https://class.coursera.org/molevol-003/lecture/15 Natural selection (14:57)]<br /> :* [https://class.coursera.org/molevol-003/lecture/17 Evidence for evolution (part 1) (9:34)] <br /> :* [https://class.coursera.org/molevol-003/lecture/19 Evidence for evolution (part 2) (20:54)]<br /> :* [https://class.coursera.org/molevol-003/lecture/35 Population growth and selection (18:13)]<br /> <br /> :; Course material<br /> :* [http://wiki.bio.dtu.dk/~agpe/course_material/27615/PDFs/lecturenotebook.pdf Lecture notes]<br /> :* [http://wiki.bio.dtu.dk/~agpe/course_material/27615/PDFs/slides_week1.pdf Slides, week 1]<br /> <br /> :; Computer exercise<br /> :* [http://www.cbs.dtu.dk/courses/27615/exercises/simulation1_courseraversion.php Population Growth, Fitness, and Selection]<br /> <br /> ----<br /> <br /> ===Week 2 (February 10): Neutral mutations and genetic drift. Tree reconstruction by parsimony===<br /> <br /> :; Online lectures<br /> :* [https://class.coursera.org/molevol-003/lecture/21 Neutral Theory of Molecular Evolution (11:28)]<br /> :* [https://class.coursera.org/molevol-003/lecture/23 Genetic Drift (9:35)]<br /> :* [https://class.coursera.org/molevol-003/lecture/25 Trees: Terminology and Representation (9:41)]<br /> :* [https://class.coursera.org/molevol-003/lecture/27 Homology and Homoplasy (9:07)]<br /> :* [https://class.coursera.org/molevol-003/lecture/29 Maximum Parsimony (7:48)]<br /> :* [https://class.coursera.org/molevol-003/lecture/31 The Fitch Algorithm (10:31)]<br /> :* [https://class.coursera.org/molevol-003/lecture/33 Searching Tree Space (14:01)]<br /> <br /> :; Course material<br /> :* [http://wiki.bio.dtu.dk/~agpe/course_material/27615/PDFs/slides_week2.pdf Slides, week 2]<br /> <br /> :; Computer exercise<br /> :* [http://www.cbs.dtu.dk/courses/27615/exercises/parsimony1_courseraversion.php Phylogenetic Analysis using Parsimony]<br /> <br /> ----<br /> <br /> ===Week 3+4 (February 17+24): Mini project 1===<br /> <br /> Building a tree from scratch: What are the closest relatives of whales?<br /> <br /> The mini project should be submitted and assessed via the [https://www.peergrade.io/login peergrade.io] interface. <br /> <br /> ----<br /> <br /> ===Week 5 (March 2): Consensus trees. Distance matrix methods===<br /> <br /> :; Online lectures<br /> :* [https://class.coursera.org/molevol-003/lecture/39 Consensus Trees (16:27)]<br /> :* [https://class.coursera.org/molevol-003/lecture/41 Distance Matrix Methods, part 1 (6:07)]<br /> :* [https://class.coursera.org/molevol-003/lecture/43 Distance Matrix Methods, part 2 (22:28)]<br /> :* [https://class.coursera.org/molevol-003/lecture/45 Neighbour Joining (15:28)]<br /> <br /> :; Course material<br /> :* [[Media:Consensus.pdf|Handout exercise: Consensus Trees]]<br /> :* [[Media:Distance handout.pdf|Handout exercise: Distance Matrix Methods]]<br /> :* [[Media:Slides week3.pdf|Slides, week 5]]<br /> <br /> :; Computer exercises<br /> :* [http://www.cbs.dtu.dk/courses/27615/exercises/consensustrees_courseraversion.php Consensus Trees]<br /> :* [http://www.cbs.dtu.dk/courses/27615/exercises/distance1_courseraversion.php Distance Matrix Methods]<br /> <br /> ----<br /> <br /> ===Week 6 (March 9): Models of sequence evolution. Likelihood methods===<br /> <br /> :; Online lectures<br /> :* [https://class.coursera.org/molevol-003/lecture/49 Models of evolution (28:48)]<br /> :* [https://class.coursera.org/molevol-003/lecture/51 Maximum likelihood (22:06)]<br /> :* [https://class.coursera.org/molevol-003/lecture/53 Ancestral reconstruction (10:45)]<br /> <br /> :; Course material<br /> :* [[Media:Handout real exp change.pdf|Handout exercise: Real, Observed, and Expected Change]]<br /> :* [[Media:Handout likelihood.pdf|Handout exercise: Computation of Likelihood]]<br /> :* [[Media:Slides week4.pdf|Slides, week 6]]<br /> <br /> :; Computer exercises<br /> :* [http://www.cbs.dtu.dk/courses/27615/exercises/distance2_courseraversion.php Models of Evolution]<br /> :* [http://www.cbs.dtu.dk/courses/27615/exercises/likelihood1_courseraversion.php Maximum Likelihood]<br /> <br /> ----<br /> <br /> ===Week 7+8 (March 16 + 30): Mini project 2===<br /> <br /> ----<br /> <br /> ===Week 9 (April 6): Bayesian inference of phylogeny===<br /> <br /> :; Online lectures<br /> :* [https://class.coursera.org/molevol-003/lecture/55 Bayesian Inference (23:48)]<br /> :* [https://class.coursera.org/molevol-003/lecture/57 Markov chain Monte Carlo (19:54)]<br /> <br /> :; Course material<br /> :* [[Media:Handout.class08.pdf|Handout exercise: Bayesian estimation of model parameter value]]<br /> :* [[Media:Slides week5.pdf|Slides, week 9]]<br /> :* [http://mgel.env.duke.edu/wp-content/publicuploads/eguchi-2008-intro-to-baysian-statistics.pdf Background reading: &quot;An Introduction to Bayesian Statistics Without Using Equations&quot;]<br /> :* [http://www.nature.com/nbt/journal/v22/n9/pdf/nbt0904-1177.pdf Background reading: &quot;What is Bayesian statistics?&quot;]<br /> :* [http://rsta.royalsocietypublishing.org/content/roypta/361/1813/2681.full.pdf Background reading: &quot;Bayesian computation: a statistical revolution&quot;]<br /> <br /> :; Computer exercise<br /> :* [http://www.cbs.dtu.dk/courses/27615/exercises/bayes1_courseraversion.php Bayesian Phylogeny]<br /> <br /> ----<br /> <br /> ===Week 10 (April 13): Testing hypotheses in a phylogenetic context===<br /> <br /> :; Online lectures<br /> :* [https://class.coursera.org/molevol-003/lecture/59 Model selection, part 1 (15:19)]<br /> :* [https://class.coursera.org/molevol-003/lecture/61 Model selection, part 2 (17:20)]<br /> :* [https://class.coursera.org/molevol-003/lecture/63 Introduction to exercise (15:24)]<br /> <br /> :; Course material<br /> :* [[Media:Slides week6.pdf|Slides, week 10]]<br /> <br /> :; Computer exercise<br /> :* [http://www.cbs.dtu.dk/courses/27615/exercises/modelselect_courseraversion.php Model selection]<br /> <br /> <br /> <br /> ----<br /> <br /> ===Week 11 + 12 (April 20 + 27): Mini project 3===<br /> <br /> ----<br /> <br /> ===Week 13 (May 4): Mini project 3 finished + questions for exam ===<br /> <br /> ----<br /> <br /> ===Old exam sets===<br /> <br /> * [http://wiki.bio.dtu.dk/teaching/index.php/27615-2011 Mini project exam]<br /> * [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam_2004.pdf Exam 2004] ([http://www.cbs.dtu.dk/courses/27615/exam_examples/exam_2004_withanswers.pdf Answers])<br /> * [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2005.pdf Exam 2005]<br /> * [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2006.pdf Exam 2006]<br /> * [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2007.pdf Exam 2007]<br /> * [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2008.pdf Exam 2008]<br /> * [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2009.pdf Exam 2009] ([[Media:Exam2009 answers.pdf|Answers]])<br /> * [[Media:Exam2015.pdf|Exam 2015]] ([[Media:Exam2015 answers.pdf|Answers]])</div>

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