Computer Methods in Molecular Evolution

MCB 371-372 / EEB 371-372. Four credits.

Instructors:
Peter Gogarten (Office TLS 73, phone 486-4061, gogarten@uconn.edu)
Paul Lewis (Office TLS 166A , phone 486-2069, paul.lewis@uconn.edu)

TA:
Olga Zhaxybayeva (Office TLS 75, phone 486-3686, olga.zh@uconn.edu)

Meeting times and places:
Mondays 2-4 p.m. TLS301, Wednesdays 1-4 p.m. M037 or by announcement

!!! First organizational meeting:
Wednesday, January 23, 1 p.m. M037 (Computer Lab in Math Building)

The course combines an introduction into molecular evolution (MCB/EEB 371, 1 credit) with practical training in data analyses with respect to molecular evolution (MCB/EEB 372, 3 credits). Participants will compile and analyze a data set of their choice as a student project.

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. Paul will teach the second part of this course (focusing on PAUP).

The course will cover the following topics:

• databank searches, BLAST and iterative BLAST searches,
• sequence alignment, sequence alignment using 3-D information,
• statistical analyses of sequence data,
• 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

The following programs will be used:

NCBI webpages, ClustalX, Swiss Protein Data Bank Viewer, PhyloWin, TREE-PUZZLE, PAUP*, MrBayes and SplitsTree.

Please contact one of the instructors, if you are not sure if this course is suitable for you.