Week 11

Topics

• MCMC Convergence
• Calculating Likelihoods on Trees
• Model Selection

Readings

MCMC Convergence

• Review Yang Ch. 7.3, 7.4, and 8.4

Calculating Likelihoods on Trees

• Yang Ch. 4.2, 4.3
• Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.

Model Selection

• Yang Ch. 4.7, 7.4
• Sullivan J and Joyce P. 2005. Model selection in phylogenetics. Annu. Rev. Ecol. Evol. Syst. 36:445-466.

Assignments

• For Thurs, March 28th, finish last week's exercise including models of rate variation
• For next Tuesday, April 2nd, complete worksheets practicing Felsenstein's pruning algorithm.