• Objective of the project
• Recommended courses
• Recommended conference to attend
• Learn to work independently

Hidden Markov Models (HMMs)

• Milestone 1: Introduction to HMMs (First half of October 2003)
• Milestone 2: Viterbi algorithm (Second half of October 2003)
• Milestone 3: Learning parameters from complete data (First half of November 2003)
• Milestone 4: Forward-backward algorithm (Second half of November 2003)
• Milestone 5: Learning parameters from incomplete data with the Baum-Welch algorithm (First half of December 2003)

Phylogenetics

• Milestone 6: Introduction to phylogenetics (January-February 2004)
• Milestone 7: Combining phylogenetic trees with hidden Markov models for detecting recombination - Maximum likelihood (March 2004)
• Midproject review
• Milestone 8: Combining phylogenetic trees with hidden Markov models for detecting recombination - Bayesian approach (MCMC) (April 2004)
• Milestone 9: Combining phylogenetic trees with hidden Markov models for modelling rate variation (May 2004)
• Milestone 10: Factorial hidden Markov model for distinguishing between recombination and rate variation (June-August 2004)
• Writing up of thesis (September-October 2004)