Course: Inferring Positive Selection (from Sequences)

Lectures

  1. To come
  2. Frequency spectrum (Tajima, Fu and Li, etc.)
  3. Codon models (Goldman, Yang and Nielsen)
  4. Polymorphism and divergence (HKA and MK tests, branch and branch-sites models)

Exercises

  1. Exercise 1: Getting in touch with the Wright-Fisher model
  2. Exercise 2: Tests based on the frequency spectrum
  3. Exercise 3: Nei and Gojobori
  4. Exercise 4: Codon models
  5. Exercise 5: Polymorphism and divergence

Required files:

Datasets:

Software

Articles

Articles to be discussed:

Second session:

Datasets to analyze

Helper tools: