frog phylogeny. Target date 9 April.
(Give me hard copy
for this one)
- 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.
- Find the best
tree under parsimony with all characters weighted equally. Root the
tree with Salamanders+ Caecilians as the outgroups.
- Do 1000 bootstrap
replicates. Compare these with the values reported in the Hay et al.
paper. and discuss the differences.
- Calculate decay
indices for the best tree.
- Turn in a final
"best tree" with labeled bootstrap values above the branch
and decay indices below the branch.
Email me a detailed
outline of your project. Name the attachment: "ProjOutline+YourLastName"
- 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.
- Tell what materials
(if any) will be used (specimens, data, etc.). Put as much of this together
as possible, now.
- Describe in moderate
detail what type of data will be collected (sequences, measurements,
- Describe what
type of analyses or thought experiments, inquiries, etc. will be done.
Last updated 3/28/02
by David Cannatella