Phylogenetics (03-327/727): Course work and policies

[Course Summary] [Course Work] [Academic integrity] [Grading] [Homework] [Exams]

Course summary

An advanced introduction to theory and practice of phylogenetic analysis (evolutionary tree reconstruction), with a focus on molecular evolution. Basic concepts will be introduced in the context of a historical survey of phylogeny reconstruction. A comprehensive introduction to phylogenetic methods will be presented, including data selection, multiple sequence alignment, character state data versus distance matrices, sequence evolution models, and the four major approaches to phylogeny reconstruction: Parsimony, Distance matrix, Maximum likelihood, and Bayesian analysis. Sources of error and methods for assessing the reliability of phylogenetic inference will be discussed. We will cover additional topics as time allows, such as phylogenetic hypothesis testing, genome scale approaches, the interface between phylogenetics and population genetics, gene tree reconciliation, horizontal gene transfer, and phylogenetic networks.

Prerequisites: Modern Biology (03-121) or Permission of Instructor

Total units: 03-327: 9 units / 03-727: 12 units

Lectures and course work

Lectures will be primarily powerpoint presentations. Lecture summaries will be posted on the syllabus page. These are not comprehensive notes and are not guaranteed to cover all the material discussed in class. You are responsible for taking notes in class and learning the material from your notes and reading assignments.

I find laptops and other electronic devices in class distracting. When I am distracted, I am a poor lecturer. For this reason, I ask you to turn off your mobile devices and close your laptops during class. In addition, evidence from learning research suggests that laptops in the classroom do not enhance the academic performance of the student using the laptop and distract students sitting around them.

Course work will include 5-7 problem sets, 4 data analysis assignments (practica) using sequence analysis and phylogenetic software, and two in-class exams and a final exam.

Assigned reading will be drawn from textbooks and the primary literature. All reading materials will be provided via the course website. You are not required to buy a text book.

Students in 03-727 will also carry out a major data analysis project, intended to familiarize the student with the practical application of principles taught in class. An in-class presentation and a short paper summarizing the results of this project will be required.

Grading policy

Due dates and late assignments

Assignments are due in class on the due date. In calculating your final score, I will drop your the lowest grade of the homework assignments, but only if all assignments have been submitted by the last day of classes. This applies to problem sets only; not to practica. Your scores on all practica will be included in the final grade. No homework scores will be dropped at midterms.

The penalty for late homework is 10% per day. No late homework will be accepted once graded homework has been returned to the class and the solution set has been posted. Extensions will be granted only in extraordinary circumstances (e.g., an extended illness). There will be no "makeup" homework assignments.

Collaboration on homework

Discussion of homework problems with other students is allowed, but each student must prepare his or her own assignment. Students may not copy any portion of a homework assignment from another student, nor may they jointly prepare all or part of an assignment. An example of acceptable collaboration would be the discussion of strategies for a particular task, followed by each student carrying out that strategy independently. Examples of unacceptable collaboration are:

  1. jointly doing an analysis and then handing in multiple copies of the results.
  2. following a method suggested by someone else without being able to explain the method.

You may consult textbooks, articles and websites while preparing your assignments. You should not follow a procedure described in such sources, unless you understand it well enough to explain it. You may not consult solution sets from previous years. Nor may you quote from any source without attribution.

Academic Integrity

All students are responsible for familiarizing themselves with the Carnegie Mellon policies on Academic Integrity, Cheating, and Plagiarism, and adhering to those policies .    In order to deter and detect plagiarism, online tools and other resources may be used in this class.

You should be aware that plagiarism, cheating and other violations of the academic integrity policy are considered to be serious infractions at Carnegie Mellon. CMU policy allows me to exact a penalty as severe as failure in the course for a single violation.

Exam policy

Exams are closed book. You may bring two 8.5"x11" pages (or one page, front and back) of your own notes. Bring a calculator. The final exam will be cumulative. You are responsible for all material covered during the semester.

The time and date of the final exam are determined by the registrar's office and are beyond my control.     Until the date of the final is determined, you should not make plans to leave for winter vacation before the end of the exam period. No student will be permitted to take the final exam early.

No student is required to take more than two scheduled examinations that start within a 25-hour period. If you have more than two final examinations scheduled within a 25-hour period or another examination scheduled at the same time as the exam for this course, please see me immediately to discuss how to resolve this conflict.

With the exception of the above, make-up exams will not be offered, except in the case of documented illness or family emergency. This policy applies to both in-class exams and the final exam.

Last modified: August 28, 2017.
Maintained by Dannie Durand (