Schedule

I will update this page before every class with the links to in-class materials and assignments. To view the planned schedule of course activities, view the class calendar using the button below.

Class Calendar

Week 1 (Jan 21, 23)

• Lecture 1: Introduction to Molecular Phylogenetics [slides]
  • Assignment 1 (due 1/23)
• Lecture 2: Trees and characters [notes]
  • Assignment 1 is due.
  • Reading: Allman and Rhodes (2016). Chapter 2: Combinatorics of Trees I.
  • Discussion: Baum et al. (2005). The Tree-Thinking Challenge. Science 310: 979-980.

Week 2 (Jan 28, 30)

• Lecture 3: Homology and Sequence Alignment [notes]
  • Reading: Chatzou et al. 2016. Multiple sequence alignment modeling: methods and applications Briefings in Bioinformatics, 17(6), 2016, 1009–1023.
  • Discussion: Gabaldón and Koonin (2013). Functional and evolutionary implications of gene orthology. Nature Reviews Genetics volume 14, pages 360–366.
    
• Computer Lab 1: Introduction to Unix/Multiple Sequence Alignment (MSA).
  • Complete all prerequisites before coming to the class!
  • Post any question you may have on Slack.
  • Assignment 2 (due 02/06)

Week 3 (Feb 4, Feb 6)

• Lecture 4: Parsimony and cladistics. Optimality criteria and character optimization.
  • Reading: Allman and Rhodes (2016). Chapter 3: Parsimony. [notes]
• Lecture 5: Searching tree space. Measures of character fit. Assessing clade support.
  • Reading: Allman and Rhodes (2016). Chapter 9: Tree Space. [notes]
  • Discussion: Baron et al. (2017). A new hypothesis of dinosaur relationships and early dinosaur evolution. Nature 543: 501-506. See also News & Views, Langer et al. communication, and Baron et al. reply.

Week 4 (Feb 11, 13)

• Computer Lab 2: Parsimony analysis.
  • You may want to install Mafft, PAUP*, and TNT on your computer [links]. However, we will use HPC-class cluster for the excercises.
  • Assignment 3 (due 02/18)
• Lecture 6: Distance matrix methods. Clustering algorithms. [notes]
  • Reading: Allman and Rhodes (2016). Chapter 5: Distance Methods.

Week 5 (Feb 18, 20)

• Lecture 7: NJ algorithm; Model-based distances. [notes]
  • Reading: (Optional!) Allman and Rhodes (2016). Chapter 6: Probabilistic Models of DNA Mutations.
  • Discussion: Naxerova et al. (2017). Origins of lymphatic and distant metastases in human colorectal cancer. Science 357, 55-60.
• Computer Lab 3: Distance analysis with PAUP, PHYLIP, and FastME.
  • Assignment 4 (due 02/27)

Week 6 (Feb 25, 27)

• Lecture 8: Introduction to Maximum Likelihood. [notes]
  • Reading: Allman and Rhodes (2016). Chapter 8: Maximum Likelihood.
• Lecture 9: Constructing Phylogenetic Trees Using Maximum Likelihood. [notes]
  • Discussion: Basem Al-Shayeb et al. (2020). Clades of huge phages from across Earth’s ecosystems. Nature 578, 425–431. If you want to brush up your knowledge on bacteriophages, here is a nice review from the same issue of Nature.

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