Until recently, the inference of the evolutionary history of currently living species was based primarily on painstaking studies of their morphological similarities, together with comparison to the fossil record. Now a vast new source of evolutionary data is available through genetic sequencing. How to infer an entire evolutionary tree from biological sequences is a rich mathematical question.

This course begins with an overview of the sorts of biological questions of interest, and a look at the nature of biological sequence data. We then develop several of the modern approaches to sequence-based phylogenetics, focusing on the modeling of the process of molecular evolution along a tree. Shortcomings of the various methods and models, both theoretical and practical, will be used to motivate new ones.

This course will provide an introduction to the mathematics of molecular phylogenetics. Necessary mathematical and biological background will be kept minimal: basic probability and linear algebra are helpful but can be picked up along the way. The course will also include elements of combinatorics, graph theory, algorithmics, Markov models and statistics, as well as hands-on computer work with real and simulated data.

Web Page
Announcements, course information and assignments will be posted on the course web page.  The URL for this course is
http://www.gac.edu/~mmcdermo/mcs255/j06/

Prerequisites
One MCS course numbered 121 or higher.

Text Course pack. Lecture notes by John Rhodes and Elizabeth Allman.

Academic Integrity
As a student at Gustavus you are expected to uphold the Honor Code and abide by the Academic Honesty Policy. A copy of the honor code and academic honesty policy can be found in the Academic Bulletin and in the Gustie Guide.

Accessibility
Please contact me during the first week of class if you have specific physical, psychiatric, or learning disability and require accommodation. I will do my best to facilitate the necessary arrangements. You can provide documentation of your disability to the Advising Center (204 Johnson Student Union). All discussions will remain confidential. Call Jane Lalim in Academic Advising (x7072).

Evaluation
I encourage you all to elect to take this course pass/fail. A passing grade will be given if you complete satisfactorily all assignments and miss no more than two class meetings.

If you elect to take this course for a letter grade, your course grade will be determined using the following percentages as a guide: