Lecture 7

Assignment for frog phylogeny. Target date 9 April.

(Give me hard copy for this one)

  1. Download the Hay data set, align it. It will probably help to re-read the Hay et al. paper. Write a couple of paragraphs explaining which regions were excluded (if any) and why.
  2. Find the best tree under parsimony with all characters weighted equally. Root the tree with Salamanders+ Caecilians as the outgroups.
  3. Do 1000 bootstrap replicates. Compare these with the values reported in the Hay et al. paper. and discuss the differences.
  4. Calculate decay indices for the best tree.
  5. Turn in a final "best tree" with labeled bootstrap values above the branch and decay indices below the branch.

Assignment for 3 April.

Email me a detailed outline of your project. Name the attachment: "ProjOutline+YourLastName"

  1. In a paragraph or two, describe what your paper will be about, but don't review the literature; no references are needed. State the hypotheses to be tested and what the general significance (not results) will be.
  2. Tell what materials (if any) will be used (specimens, data, etc.). Put as much of this together as possible, now.
  3. Describe in moderate detail what type of data will be collected (sequences, measurements, etc.).
  4. Describe what type of analyses or thought experiments, inquiries, etc. will be done.


Last updated 3/28/02 by David Cannatella