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This course involves weekly homework assignments that you are expected to complete without consulting with other students, but you are welcome (encouraged!) to consult with the instructors. Some homework assignments will involve hand calculations (using an actual or online calculator), some will involve a small amount of computer programming in Python and R (but note that no previous programming background is assumed), and others will involve small projects that require you to understand how to set up software such as RevBayes to carry out an analysis, and then report on what you found.


Labs involve self-paced tutorials designed to teach you how to use important phylogenetics software packages and how to carry out analyses remotely using the Xanadu cluster. For each lab you will need to turn in something to demonstrate that you worked through the lab exercise.


The course will be to some degree “flipped” in that I will assign reading from the textbook or papers from the literature and expect you to have read it before lecture. You receive participation credit for asking questions and participating in discussions about the material you’ve read, or material presented in either lecture or lab. I realize not everyone is comfortable actively participating in class, so one or more questions may be submitted via email before lecture if that is better for you.

Due Dates and Late Policy

Because there are no formal exams, term papers, or projects, it is important to not skip or get behind on the homework assignments. You will be given 1 week to complete a homework assignment (i.e. until midnight on the Tuesday after it is assigned).

Every day after that you will lose 1 point on the homework assignment (so 10 days late means 0 for that assignment). For example, if you turn in your homework at any time on the Wednesday following the Tuesday due date, you will lose 1 point.

It is best to turn in your answers to lab exercises on the day of lab, but, if you don’t get finished during the allotted lab time, you can turn them in as late as midnight on the Sunday following the Thursday lab. After that, 1 point will be deducted for each day. For example, if you turn in your lab assignment on the Monday following the lab, you will have 1 point deducted.


Percentage Points Description
70.6 120 Homeworks (10 each)
21.2 36 Lab activities (3 each)
8.2 14 Participation
100.0 170 Total

Grading scale

At least Less than Letter grade
93% 100% A
90% 93% A-
87% 90% B+
83% 87% B
80% 83% B-
77% 80% C+
73% 77% C
70% 73% C-
67% 70% D+
63% 67% D
60% 63% D-
0% 60% F