22115 - Computational Molecular Evolution

From 22115
Jump to: navigation, search
Overview
Darwin logo2 medium.png
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 will 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. Because of this setup we ask that you please install the virtual machine even if you are already running Linux.
  • 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).
  • MolEvol_2020_Clone.zip: Virtual Disk Image file (compressed) containing pre-installed Linux (Ubuntu) operating system and all software needed for this course.
  • 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

(Course programs, previous years)

Week 1 (February 5): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation

Online lectures
Course material
Computer exercise

Week 2 (February 12): Neutral mutations and genetic drift. Tree reconstruction by parsimony

Online lectures
Course material
Computer exercise

Week 3+4 (February 19+26): Mini project 1

Building a tree from scratch: What are the closest relatives of whales?

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


Week 5 (March 4): Consensus trees. Distance matrix methods

Online lectures
Course material
Computer exercises

Week 6 (March 11): Models of sequence evolution. Likelihood methods

Online lectures
Course material
Computer exercises

Week 7+8 (March 18 + 25): Mini project 2

Comparison of tree building methods and codon-based alignment - The origin of Lassa virus epidemics.

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


Week 9 (April 1): Bayesian inference of phylogeny

Online lectures
Course material
Computer exercise

Week 10 (April 15): Testing hypotheses in a phylogenetic context

Online lectures
Course material
Computer exercise



Week 11 + 12 (April 22 + April 29): Mini project 3


Week 13 (May 6): Mini project 3 finished + questions for exam


Old exam sets