Computer Methods in Molecular Evolution
Instructor: J. Peter Gogarten (Office BPB 404, phone 486-4061, firstname.lastname@example.org)
Meeting times and places:
Lecture and Demonstrations, BPB 401, Mondays 1pm - 2.30 pm .
Computer Lab (Chemistry T115): Wednesdays 1pm - 2.50 pm
!!! First meeting: Wednesday, January 20, 1 pm in T115 !!!
The course provides practical training in data analyses with respect to molecular evolution.
The course is open to advanced undergraduates with permission of
The course will cover the following topics:
- databank searches,
BLAST and iterative BLAST searches,
- simple Perl scripts to
process genome scale amounts of data
- use of the UNIX clusters at the Bioinformatics services facility
- sequence alignment (clustalx, muscle, ...)
- 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, Bayesian posterior probabilities, and split
- detection of positive
and purifying selection
- detection of gene transfers and lineage specific duplications
- screening genomes for molecular parasites
- aligning genomes using gene plot, mummer, and mauve
are required to complete a student project
(this project can be related to the student's resarch).
Please contact the instructor (email@example.com 860 486 4061), if you are not sure if this course
is suitable for you.
Gogarten Lab: http://gogarten.uconn.edu; Class homepage: http://gogarten.uconn.edu/mcb5472