General Course Information

• Syllabus
• Updated Schedule -- posted April 27, 2010: pdf

Copies of lecture slides (pdf)

• Lecure 1 -- March 30, 2010 :::: Slides, Handout
• Lecture 2 -- April 6, 2010 :::: Slides
• Lecture 3 -- April 20, 2010 :::: Slides, Handout
• Lecture 4 -- April 27, 2010 :::: Slides
• Lecture 5, Part 1 -- May 4, 2010 :::: Slides
• Lecture 5, Part 2 -- May 4, 2010 :::: Handout
• Lecture 6 -- May 11, 2010 :::: Slides
• Lecture 7 -- May 18, 2010 :::: Slides
• Lecture 8, Part 1 -- May 25, 2010 :::: Slides
• Lecture 8, Part 2 -- May 25, 2010 :::: Slides
• Lecture 9 (continuation of Lecture 8, Part 2) -- May 27, 2010 :::: Slides

• Lab 1 -- April 1, 2010 :::: Handout
• Lab 2 -- April 8, 2010 :::: Handout, Slides
• Lab 3 -- April 22, 2010 :::: Handout
• Information on drawing trees in UNIX :::: Handout
• Lab 4 -- April 29, 2010 :::: Handout
• Lab 5 -- May 6, 2010 :::: Handout
• Lab 6 -- May 13, 2010 :::: Handout
• Lab 7 -- May 20, 2010 :::: Handout
• Lab 8 -- May 27, 2010
  R code for comparative method example
  Example paper: Butler and King (2004)

• HW #1 - due Thursday, May 6, in class
  • NEXUS data file for HW #1
• Solutions to HW #1

• primates data (in NEXUS format)
• HPV data (in NEXUS format)
• Yeast data:
  • rokas14_sequential.nex (in NEXUS format)
  • rokas14_interleaved_mb.nex (in NEXUS format)
  • yeast.nex
• modelblockPAUPb10
• mammals.fas
• COALexamples.zip
• Finch data

• PAUP*
• ModelTest
• GARLI
• MrBayes
• COAL
• BEST

• Enzyme data (Prof. Pearl)
• Palaeoptera explanation (Rasmus Hovmoller)
  Associated papers:
  • Hovmoller et al. (pdf)
  • Odgen and Whiting (pdf)