Computer Methods in Molecular Evolution
Paul Lewis (Office TLS 166A , phone 486-2069, plewis@uconnvm.uconn.edu)
MCB 372 / EEB 372. Three credits.
Meeting times Mondays 12-1 p.m., Wednesdays 10 a.m. – 12 p.m.
Meeting place: New MCB Mac lab, 3rd floor LSA 306
!!! First organizational meeting: Wednesday, January 26, 3 p.m. LSA 306 !!!
The course is designed to teach practical aspects of molecular data analyses with respect to molecular evolution. Students will compile and analyze a data set of their choice. The course does not provide an introduction into molecular evolution, and it is not a place for discussions of problems related to cladistics. Students lacking background in molecular evolution should ask the instructors for recommended supplementary reading material.
The course is open to advanced undergraduates with permission of one of the instructors.
Paul Lewis is a new faculty member in the EEB department. He is interested in genetic algorithms, 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 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, PUZZLE,
PAUP*, BAMBE, PAML, GAML, and SplitsTree.
Please contact one of the instructors, if you are not sure if this course is suitable for you.