3 hours credit
10 students maximum

This advanced course focuses primarily on the myriad problems
of multiple sequence analysis and the methods that have been
developed to describe molecular phylogenetics and evolution.
Multiple sequence analyis is introduced in the Introductory
Sequence Analysis Course but because the subject is a complex
one, an in-depth approach is deferred until this second course.
The goal of this second course is to introduce the student to
a large number of tools designed for molecular phylogenetics
and evolution including CLUSTALW, TreeALIGN, PAUP, MACCLADE,
DNAStacks, and the PHYLIP program suite. The concepts covered
include Distance methods, Parsimony methods,
maximum-liklihood methods, Lake invariant methods. Students
are required to chose a series of sequences of interest to
them. Multiple alignments are constructed, evaluated, revised
and re-interprettd with an ultimate goal of establishing whether
the various analytical tools produce congruent phylogenies.

The course will include, but not necessarily be limited
to the following topics:

Advanced Multiple Sequence Alignment
Advanced Prosite/motifs searching
Detailed Profile searching
Models of molecular evolution
Phylogenetic analysis by distance, parsimony and maximum
liklihood methods

The Introductory Sequence Analysis Course is a prerequisite for
this course. This course will consist of a series of three
lab/lectures/discussion periods per week. Students will be
required to propose, prepare and present to the rest of the class,
a semester project relevant to their research interests. Grades
will be based on class participation, and the semester project
report.