Computer Intensive Methods in Phylogeny

Spring 1998 - Biometry 682
Web site:http://www-stat.stanford.edu/~susan/phylo/index/

TR 1.25-2.15, 2 units, Instructor: Susan Holmes
Copyright 1998

• Logistics
  • Outline
  • Tentative Project Groups
  • Labs and Potential Projects
    • Lab. 1
    • Lab. 2
    • Lab. 3
    • Lab. 4
    • Biometry 682 - Lab. 5
• Lecture Summaries
  • Introduction
  • Randomness
  • The Bootstrap:Motivations
    • The bootstrap : the univariate context
      • In practice
    • Parametric bootstrap
    • Smoothed Bootstrap
    • Different Uses for bootstrapping
      • Quality of Estimates
    • Enhancements
    • Bootstrap-t : Studentizing
    • Preliminary Transformations of the Estimate
    • Pre-pivoting or Double Bootstrap
  • The Substitution Model
  • Maximum Likelihood Methods for Estimating Trees
  • Representation of trees
  • Bayesian Approach to statistics
    • About Priors
      • Calibrating degrees of belief
    • Examples
    • Beta priors for the Binomial parameter
    • Monty Hall example of use of using prior information
  • The Bayesian Approach for the Tree Problem
  • More about the data
    • From sequences to Distances
    • Distance Based Methods
    • Sparsity
  • More about trees
    • Minimum Spanning Trees
    • Steiner Trees
    • Branch and Bound
    • A binary coding
  • Validating Tree building methods
    • Error
    • Long branches
    • Non-additivity
    • Incorrect parametric model
    • Sensitivity to specific taxa
  • The Bootstrap
    • Sometimes the Bootstrap Behaves Badly
    • Curvature of a confidence region
      • Estimation of CART Bias
    • Multivariate Regression
  • Comparing Trees
    • Distances between Trees
    • Testing similarity between data sets
      • Testing the evolutionary hypothesis
    • Testing similarity between distances
    • Permutation tests for Correlation
      • Are two variables correlated?
    • Comparing two distances
    • The earwig example
• References
  • The Web Sites: a virtual library
• References
• About this document ...