Lecture plan

This is a tentative lecture plan!

1. Intro: Biology and CS, terminology and prerequisites. Aligning sequences.
2. Pairwise alignments
3. Affine gap scores. Scoring systems and models.
4. Linear space alignments. (Pages 35-36.)
5. The multialignment problem. (Pages 135-149.)
6. Heuristics for local alignments. (Pages 33-34.) NC score and what do we really want? (Song and Durand.)
   HW1 due.
7. Mapping and filtering of DNA reads.
8. Hidden Markov Models for analyzing sequences.
9. EM and HMM training
   HW2 due.
10. Phylogenetics. The parsimony method.
11. Distance methods, NJ
12. Tree reconciliation
    HW3 due.
13. MCMC methods for phylogeny
14. Case study: The PrIME project for phylogenetic inference.

HW4 due after the last lecture.