Analytical methods: Assessing Confidence

What gives confidence?

Random Permutation Methods

Nonparametric Bootstrapping (often just called 'Bootstrapping')

  1. Build a new data matrix by randomly sampling characters with replacement
    1. Take the original data matrix
    2. Sample the matrix, randomly copying one character (column) from the original matrix
      • Do not delete the character after copying it
      • Each taxon's character state for the sampled character remains as it was in the original matrix
    3. Add the selected character to a new data matrix
    4. Repeat sampling until the new data matrix has as many characters as the original
      • Some characters will be sampled more than once, others not at all
      • The new dataset (a pseudosample) contains the same number of characters as the original data set, and the taxa included are unchanged.
  2. Perform full phylogenetic analysis
  3. Repeat many times
  4. Calculate frequency with which taxon bipartitions (branches) appear in the new analyses (these frequencies are often reported as percentages)


Hypothesis Testing