Pairwise Alignment

• Required readings: The entire chapter 2 of the BSA textbook.
• Essential readings: Ch2.1-Ch2.3, Ch2.7
• Optional readings: chapter 6 of the CMB textbook

Multiple alignment

• Required readings: Pages 134-149 of Chapter 6 of the BSA textbook, and the ClustalW paper.
• Optional readings: chapter 7 of the CMB textbook

Hidden Markov Models: Basics

• Required readings: Pages 46-66 of Chapter 3 of the BSA textbook.
• Optional readings: Pages 66-78 of Chapter 3 of the BSA textbook.

Hidden Markov Models: Applications

• Required readings: Sections 5.2, 5.3, and 5.4 of Chapter 5 and Section 6.5 of Chapter 6 in the BSA textbook.
• Optional readings: Other sections of Chapter 5 of the BSA textbook.

Phylogenetic Tree Construction

• Required readings: Sections 7.1-7.4 of Chapter 7 and Sections 8.1-8.4 of Chapter 8 in the BSA textbook.
• Essential readings: Sections pages 166-176 and pages 192-202.
• Optional readings: Other sections of Chapter 7 and Chapter 8 of the BSA textbook.

Pattern Discovery

• Background readings (Two excellent survey articles)
  • Approaches to the automatic discovery of patterns in biosequences
  • Finding Patterns in Biological Sequences
• Core algorithm readings (not required):
  • SPLASH Algorithm
  • Gibbs Sampling Algorithm
• Notes: These readings are fairly advanced, so you are not expected to fully understand them. Read whatever seems to be interesting to you. Try to read at least one survey article, though.