Multiple
Sequence Alignment: Case Studies.
Small
version,
larger version.
A lecture by Hugh Nicholas at
the PSC describing techniques for
obtaining a biologically correct multiple alignment, illustrated
by case studies, including families more challenging than the
Estradiol data set used in class. This lecture
is optional. 03-737 students are likely to find these
techniques useful for completing their projects, as will any
student attempting to align protein sequences for research or
course work.
Readings on tree methods: Page and Holmes,
- Introduction to tree methods (6.1.0 - 6.1.3), pp. 172-178.
- Discrete methods (6.3) and Parsimony (6.4.0 - 6.4.3), pp. 187-191
- Distance based methods (6.2.0-6.2.3), pp. 179-185.
- Maximum likelihood (6.5.0-6.5.2), pp. 183 - 196.
- Comparing tree methods
- Bases for comparison (6.1.4), pp. 178 - 179.
- Pbs with distance methods (6.2.4), pp. 185 - 187.
- Parsimony, Likehihood (6.5.3, 6.5.4), pp. 199 - 201