Computer Methods in Molecular Evolution
MCB 371-372 / EEB 371-372.
Four credits.
Instructors:
Peter Gogarten (Office BSP 404, phone 486-4061, gogarten@uconn.edu)
Paul Lewis (Office TLS 166A , phone 486-2069, paul.lewis@uconn.edu)
Meeting times and places:
Lecture and Demonstration: Mondays and Wednesdays 11am -12.15 pm TLS 179.
Computer Lab: Mondays 1pm-3pm
Location will change for the second half of the semester.
!!! First meeting: Wednesday, January 19, 11 a.m.
in TLS 179 !!!
The course combines an introduction into molecular evolution (MCB/EEB 371)
with practical training in data analyses with respect to molecular evolution
(MCB/EEB 372). Participants need to sign up for both 371 and 372!
The course is open to advanced undergraduates with permission of one of
the instructors.
Paul Lewis is a faculty member in the EEB department. He is interested in
application of Bayesian inference to systematics, he has many years of
experience in working with PAUP, and above all he has excellent skills in
communicating complex mathematical approaches to biologists. He will teach
the first part of this course (focusing on PAUP and MrBayes).
Peter Gogarten is a faculty member in MCB. He is interested in microbial evolution, gene
duplications, horizontal gene transfer, and comparative genome analyses. His part of the course will focus on
tools to analyze large amounts of data.
The course will cover the following topics:
- phylogenetic reconstruction
using parsimony -, distance matrix -, maximum likelihood, bayesian
inference and other methods
- likelihood ratio tests
for model selection
- Assessment of
confidence using maximum likelihood mapping, bootstrapping, Bremer
support/decay index, Bayesian posterior probabilities, and split
decomposition
- databank searches,
BLAST and iterative BLAST searches,
- simple PERL scripts to
process genome scale amounts of data
- detection of positive
and purifying selection
Students
are required to complete a student project.
Please contact one of the instructors, if you are not sure if this course
is suitable for you.
Gogarten Lab: http://gogarten.uconn.edu
Lewis Lab: http://hydrodictyon.eeb.uconn.edu/people/plewis/
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