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syllabus - BSC 5936-6(CRN 11476 Fall 2005 SPECIAL TOPICS...

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BSC 5936-6 (CRN: 11476) Fall 2005 SPECIAL TOPICS: Computational Evolutionary Biology Class Meeting Lectures: Mondays and Wednesdays 0905-1015 Dirac Science Library Room 156 Lab-session: Mondays 1100-0100 Dirac Science Library Room 156 Instructors Fredrik Ronquist Peter Beerli 150-S DSL 150-T DSL [email protected] [email protected] 645-1325 645 1324 Office Hours Monday 0100-0300 or by appointment. Objectives This course will introduce students to methods used in phylogenetics and population genetics and writing computer programs using such methods. Primary objectives of the course are: 1. to expose students to a large set of modern methods used in the field of theoretical evolu- tionary biology 2. introduce students to the programming aspects of the field 3. enable students to develop software that is a base for further exploration or incorporation of new methods. Content Advanced computational methods are becoming increasingly important in biology. A wide range of applications — including, for instance, identifying pathogens, tracing viral transmission pathways, and reconstructing the geographic expansion of humans out of Africa — rely on evolutionary infer- ence. This course will cover the methods currently used for evolutionary inference, the stochastic models and inference principles they are based on, and how they are implemented in practice. In a separate lab session, the students will get hands-on experience in developing computational software implementing these methods. We expect that the students leave the course with the necessary skills to develop their own ideas and methods. 1
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BSC 5936-6 (CRN: 11476) Fall 2005 Textbook Felsenstein, Joseph. 2004. Inferring Phylogenies. Sinauer, Sunderland MA (we did not preorder the books through the bookstore, we recommend ordering it through amazon.com, much faster than ordering directly from Sinauer) The textbook includes material for almost all of the major topics that we expect to cover. There is a small amount of material that will be presented in class that is not covered by the textbook. This
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