Introduction to Phylogenies and Probability (Week 3)

This week, we will cover some fundamentals of:

• Reading and interpreting phylogenies
• Probability theory

Week 3 Assignment

• Find a moderately sized tree (~20-50 tips) in a published paper.
• Go download the text description of that tree (hopefully it's available, but not all journals require them to be). These are often located in TreeBase or Dryad.
• Examine the text file you downloaded. What format is it in? Is there any other information in the file?
• Open the file in FigTree and adjust the settings so that the tree and labels are legible.
• Now, reformat the tree (size, style, coloring, etc.) so that the main points made in the paper about the relationships of interest are obvious. It doesn't need to look like the publication, but you should be able to see the take-home message.
• Export the tree as a pdf, save the file, and commit it to the "trees" folder of your fork of this week's repository. Then submit a pull request to the class page.
• Also save and commit a simple text file with a reference to the paper where you got the tree.