Lecture plan

This is a tentative lecture plan, and subject to change.

* Intro: Biology and CS, terminology and prerequisites.
* Pairwise alignments
* Local alignment, affine gap costs
* The multialignment problem. (Pages 135-149.)
* Heuristics for local alignment (pages 33-34, Slides on Blast) and the Burrows-Wheeler transform for fast searches
* The multialignment problem. (Pages 135-149.)
* Protein clustering: NC score and what do we really want? Filtering of DNA reads
* Hidden Markov Models for analyzing sequences.
* More on HMMs
* EM and HMM training
* Phylogenetics. The parsimony method.
* Distance methods, NJ
* Tree reconciliation.
* Genome assembly
* More on genome assembly