I will be offering a course this winter listed as EEB 491 Phylogenetic
Systematics covering phylogenetic methods and theory. Basically, the
idea is to learn the procedures used in phylogenetics (e.g., sequence
alignments, phylogenetic reconstruction, analyses on trees, etc.) by
going through the algorithms and simple python programming. Each class
will consist of a discussion of a particular topic followed by an
examination of the algorithm using python. Although we will explore
these concepts through practical programming, prior programming
knowledge is not required and we will go over basic programming
concepts at the beginning of the course. However, students should be
familiar with text editors and running things in the terminal or
shell. For those looking for a good resource before class, I would
recommend Practical computing for biologists by Haddock and Dunn.
Please pass this information along to anyone who may find this useful
(class description below).
EEB 491 Phylogenetic Systematics
Time Wed. 10:00am-1pm ; 4 Credits; Winter 2013
Location 3427 MH
EEB 491 is a course designed to cover theory and methods used in
phylogenetics. In addition to discussions of each topic, students will
learn the material by examining the algorithms with the python
programming language. Classes will consist of a description and
discussion of the topic followed by implementations of the algorithm
in python. The goal is for students to understand phylogenetic methods
through practical programming experiences. Topics will includes
sequence manipulation and alignment, dataset assembly, phylogenetic
reconstruction, tree searching, character reconstruction, and dating
analyses. Prior programming experience is helpful but is not required.
Class will start with a python tutorial and students will learn or
strengthen programming skills throughout the course. However,
familiarity with computers is assumed (e.g., ability to use text
editors, navigate and run programs in the shell or terminal) and
tutorials will be available through the course website. Weekly
homework will be given and will typically involve extending the
procedures covered in class. Students will also develop a project of
their own involving either the exploration of a method or analysis of
their own data. Students need to have a laptop available to them for
class.
For more information (syllabus, tutorials for computer use, etc.) see
http://blackrim.org/teaching/
Suggested texts [tentative]:
Computational molecular evolution, Ziheng Yang
Biological sequence analysis, Durbin et al.
If you have any questions, feel free to ask
Take care,
Stephen
