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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,..."

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; Overview [[File:Darwin logo2 medium.png |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, 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 micro-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:
:In this course we will use software running on a Linux platform. You can do this by installing Oracle VirtualBox and then using the virtual disk image we have prepared for you (see links below). The virtual disk image contains both a pre-installed Linux operating system and all the software you will need to do the weekly computer exercises. If you are already running Linux (or a Linux-like operating system like MacOS) you may want to experiment with directly installing on your own computer (see instructions below), but then you have to sort out the installation issues yourself (the alternative is to install the virtual Linux on top of your own Linux, which also works).

:*[https://youtu.be/xaKQDN2PMtc '''Quick-start (video)''']: How to install and use the virtual machine (shown on Mac OSX, but other platforms will be very similar). (Note: instruction video is for Coursera version of course, but it should be simple to extrapolate to your own situation).
:* [https://files.dtu.dk/u/nnYXkqf2F4yMdheQ/MolEvol_2021.zip?l MolEvol_2021.zip]: Virtual Disk Image file (compressed) containing pre-installed Linux (Linux Lite) operating system and all software needed for this course.
:** Compressed file size: 4.5 GB
:** Full file size: 12 GB (maximum size: 30 GB, dynamically allocated, so size only increases as needed.)
:** Linux distribution used here is Linux Lite. Should be fairly simple to use (note the app start window in lower left corner, which works much like on Windows)
:** List of software used (in case you want to install on own operating system): [[Software installation instructions]]
:*[https://www.virtualbox.org/wiki/Downloads '''Oracle VirtualBox''']: Download and install the version for your operating system. Allows use of guest operating system (Linux) on top of your main operating system (typically Windows, Mac OSX, or Linux).

:The default user-ID and password on the virtual machine: user-ID = student, password = 1234

== '''Lecture Schedule''' ==

:([[27615 Previous course programs|Course programs, previous years]])

===Week 1 (February 3): 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
:* [[Media:Lecturenotebook small.pdf|Lecture notes]]
:* [http://teaching.healthtech.dtu.dk/material/36615/slides_week1.pdf Slides, week 1]

:; Computer exercise
:* [[Population Growth, Fitness, and Selection]]

----

===Week 2 (February 10): 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
:* [http://teaching.healthtech.dtu.dk/material/36615/slides_week2.pdf Slides, week 2]
:* [http://teaching.healthtech.dtu.dk/material/36615/Paup_Doc_31.pdf PAUP 3.1 manual (note: for older version - contains explanations of parsimony and tree moves)]
:* [http://teaching.healthtech.dtu.dk/material/36615/PAUP4-manual.pdf PAUP 4beta command reference]

:; Computer exercise
:* [[Phylogenetic Analysis using Parsimony]]
----

===Week 3+4 (February 17+24): Mini project 1===

Project description: [[Media: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:
* [[Media:Treequiz1.pdf|Tree quiz]]
Check your replies here:
* [[Media:Treequiz1 answers.pdf|Tree quiz with answers]]

----

===Week 5 (March 3): 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
:* [[Media:Consensus.pdf|Handout exercise: Consensus Trees]]
:* [[Media:Distance handout.pdf|Handout exercise: Distance Matrix Methods]]
:* [[Media:Slides week3.pdf|Slides, week 5]]

:; Computer exercises
:* [[Consensus Trees]]
:* [[Distance Matrix Methods]]

----

===Week 6 (March 10): 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:Handout real exp change.pdf|Handout exercise: Real, Observed, and Expected Change]]
:* [[Media:Handout likelihood.pdf|Handout exercise: Computation of Likelihood]]
:* [[Media:Slides week4.pdf|Slides, week 6]]
:* [http://teaching.bioinformatics.dtu.dk/material/36615/substitutionmodels.pdf Lecture notes: Substitution models]
:* [http://teaching.bioinformatics.dtu.dk/material/36615/main.pdf Optional lecture notes: Matrix exponentials for Markov chains]
:; Computer exercises
:* [[Models of Evolution]]
:* [[Maximum Likelihood]]

----

===Week 7+8 (March 17 + 24): Mini project 2===

'''Maximum likelihood and R-based phylogenetics - The origin of the Lassa and SARS-CoV-2 virus epidemics'''

'''Lassa data set''': [https://files.dtu.dk/u/stV-fYtVfmeg1X5_/lassa.nexus?l lassa.nexus]
: Alignment of Lassa virus sequences encoding the transmembrane glycoprotein complex (GPC). GPC is important in the initial contact of the virus with the cells it infects and also its diffusion into the host cell. The 35 sequences include both rodent and human sequences, from a range of years, and a range of geographic locations. Names indicate location (Nig = Nigeria, Sier = Sierra Leone, Ivory = Ivory Coast, Lib = Liberia), year sampled, and host species (homo = human, nat = Mastomys natalensis, a rodent). You should use the "pinneo" strain from 1969 to root the tree (the "Pinneo" or "LP" strain of Lassa virus was isolated from [https://www.astmh.org/blog/october-2012/astmh-remembers-penny-pinneo,-a-pioneer-in-combati the blood of Penny Pinneo], a Pioneer in Combating Lassa Fever, after a severe hemorrhagic illness acquired in Nigeria in 1969).

'''SARS-CoV-2 data set''': See instructions in project description.

'''Project description''': [https://files.dtu.dk/u/znAAkPfwAIjccACS/Miniproject2_corona.pdf?l Miniproject2_corona.pdf]

The mini project should be submitted and assessed via the peergrade interface at DTU Learn.

----

===Week 9 (April 7): 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
:* [[Media:Handout.class08.pdf|Handout exercise: Bayesian estimation of model parameter value]]
:* [[Media:Slides week5.pdf|Slides, week 9]]
:* [[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?"]
:* [http://rsta.royalsocietypublishing.org/content/roypta/361/1813/2681.full.pdf Background reading: "Bayesian computation: a statistical revolution"]

:; Computer exercise
:* [[Bayesian Phylogeny]]

----

===Week 10 (April 14): 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
:* [[Media:Slides week6.pdf|Slides, week 10]]
:* [https://github.com/ddarriba/jmodeltest2/files/157130/manual.pdf jmodeltest manual]

:; Computer exercise
:* [[Model selection]]

----

===Week 11 (April 21): 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/ Post-processing and improving performance]

:; Computer exercise
:* [[Bayesian phylogenetics: checking convergence]]
:* [[Bayesian phylogenetics: clock models]]

----

===Week 12 + 13 (April 28 + May 5): Mini project 3===
'''Bayesian and likelihood-based phylogenetics.   SARS-CoV-2: selection and clock models'''

'''Project description''': [http://teaching.bioinformatics.dtu.dk/material/36615/Miniproject3_corona.pdf Miniproject3_corona.pdf]

The mini project should be submitted and assessed via the peergrade interface.
----

==Old exam sets==

* [http://wiki.bio.dtu.dk/teaching/index.php/27615-2011 Mini project exam]
* [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])
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2005.pdf Exam 2005]
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2006.pdf Exam 2006]
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2007.pdf Exam 2007]
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2008.pdf Exam 2008]
* [http://www.cbs.dtu.dk/courses/27615/exam_examples/exam2009.pdf Exam 2009] ([[Media:Exam2009 answers.pdf|Answers]])
* [[Media:Exam2015.pdf|Exam 2015]] ([[Media:Exam2015 answers.pdf|Answers]])

Computational Molecular Evolution 22115 - 2021 - Revision history