1. Pattern frequency demo
  2. Optimizing branch lengths using ML
  3. Comparing trees using ML requires branch length optimization
  4. Parsimony informative-pattern frequency demo
  5. Bootstrapping in phylogenetics
  6. Bootstrapping in parsimony-informative pattern frequency space demo
  7. How the P-value depends on the per-site likelihood difference distribution

Back to the demo table of contents...

Source code at https://github.com/mtholder/mephytis

Thanks to the U.S. National Science Foundation and the Heidelberg Institute for Theoretical Studies for support.