Week 12

Topics

• Nonparametric Bootstrapping
• Topological Hypothesis Testing
  • Parametric Bootstrapping
  • KH, SH, and AU Tests
  • Bayes Factors

Readings

Required

• Yang Ch. 5.4
• Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:783-791.
• Goldman N, Anderson JP, Rodrigo AG. 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49:652-670.

Optional

• Hillis DM, Bull JJ. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
• Soltis PS, Soltis DE. 2003. Applying the bootstrap in phylogeny reconstruction. Stat. Sci. 18:256-267.
• Huelsenbeck JP, Crandall KA. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-466.

Assignments

• Make sure you have identified the dataset and general analysis type that you want to use for your final project.
• Model Selection and Nonparametric Bootstrapping
  • Download and install IQTree
  • Use the same primates dataset you used for the RevBayes exercise on gene-tree inference
  • Perform model selection with AIC and BIC in IQTree and record the models they choose
  • Using the model chosen by AIC, estimate the ML tree for these data and perform non-parametric bootstrapping with 200 replicates
  • Briefly describe the results of your analysis in a text file.
  • Submit your summary and relevant output files to the homework folder (by placing them in a folder with your name and submitting a pull request).