Computer Methods in Molecular Evolution

MCB 372, three credits.

Instructor: J. Peter Gogarten (Office BPB 404, phone 486-4061, gogarten@uconn.edu)
Teaching Assistant: Tim Harlow t.harlow@uconn.edu

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 23, 1 pm in BPB 401 !!!
      (note: the 1st meeting will not take place in T115)

The course provides practical training in data analyses with respect to molecular evolution. Participants should be familiar with basic concepts in phylogenetics (or they need to be willing to do supplementary readings).
The course is open to advanced undergraduates with permission of the instructor.

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 decomposition
• 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
  
• students are required to complete a student project
  (this project can be related to the student's resarch). 
  

Please contact the instructor (gogarten@uconn.edu 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/MCB372