'Bayesian methods for phylogenetic trees' - MATH 396 Undergraduate Research Project Application Form.

INSTRUCTIONS - PROFESSORS: Please review this form. Complete or correct the sections, as applicable, from "Supervisor's Name" to "Ethics, safety, and training". Please sign and date near the bottom ("Supervisor's signature").

INSTRUCTIONS - STUDENTS: You may receive this form by email, or you may download it from www.mcgill.ca/science/research/ours/396 after it has been posted. Either way, print and review this form. Complete or correct the sections, from "Student's Name" to "Student's Level", and sign ("Student signature). Ask your supervisor to sign her/his section near the bottom. Take it to the department corresponding to the course number; this may or may not be your own department. Do not register for a '396' course on Minerva until you receive departmental permission. Have a discussion with your supervisor about time/work expectations, keeping in mind that this is a 3-credit course (roughly, 10 hours per week for 12 weeks). Remember that a '396' course is an elective.

INSTRUCTIONS - DEPARTMENTS: After the unit chair/director/designate approves (or not) this project, please notify student. If approved, please give student permission to register on Minerva, and fax this form (with signatures) to the Office for Undergraduate Research in Science at 514-398-8102. The Office for Undergraduate Research in Science will later post the project online at www.mcgill.ca/science/research/ours/396/listing, indicating whether the project is open for students to apply or taken.

QUESTIONS OR FEEDBACK? Contact Victor Chisholm by email, or phone 514-398-5964

Supervisor's Name: Russell Steele

Supervisor's Email: steele [at] math.mcgill.ca

Supervisor's Phone:

Supervisor's Website: http://www.math.mcgill.ca/steele

Supervisor's department: Mathematics and Statistics

Course number: MATH396 (Mathematics and Statistics)

Term: Fall 2011-2012

Project start date: Wednesday, September 1, 2011

Project end date: Tuesday, December 6, 2011

Project title: Bayesian methods for phylogenetic trees

Project description:

In this project, the student will be developing software to use Bayesian statistical methods for estimating phylogenetic trees. The final project of the course will be a written report comparing Bayesian approaches to phylogenetic tree estimation to non-Bayesian alternatives (maximum likelihood and maximum parsimony). The student will compare the approaches for both simulated data and a real data set from the UCSC Genome project.

Project meetings: The student will have one schedule meeting per week with the supervisor for 1.5 hours and additional meetings as necessary.

Project outline:

Weeks 1 -3: Student will learn fundamentals of Bayesian inference and Bayesian computation.

Weeks 4-6: Student will read papers on existing Bayesian approaches to phylogenetic tree estimation and will select, with supervisors' guidance, an appropriate Bayesian model (or Bayesian models) to use for the real data problem at hand.

Weeks 8-10: The student will implement the Bayesian model (or models) and test on simulated data where the true answer is known. The student will compare the performance of the Bayesian approach to maximum likelihood and maximum parsimony approaches (already implemented in publicly available software packages).

Weeks 11-13: Student will compare the results of the above approaches for the real data set and finish the writing of the final project.

Prerequisite: 1 term completed at McGill + CGPA of 3.0 or higher; or permission of instructor.

Grading scheme (The final report must be worth at least 50% of final grade): Final grade shall be based on performance and participation during meetings as evaluated by the research supervisor (20%), the implementation code for the Bayesian algorithms (30%), and the final written research report (minimum 10 pages) graded by the supervisor (50%).

Project status - This project is: Taken. The professor has no more '396' projects this term.

How students can apply: N/A; this project is filled.

Ethics, safety, and training: Supervisors are responsible for the ethics and safety compliance of undergraduate students. Which of the following, if any, is involved? None of the above (NEITHER animal subjects, nor human subjects, nor biohazardous substances, nor radioactive materials, nor handling chemicals, nor using lasers)

Student's Name:

Student's McGill ID:

Student's Email (first.last [at] mail.mcgill.ca):

Student's Phone:

Student's Program:

Student's Level (U0 / U1 / U2 / U3):

Student's signature - I have not applied for another '396' course in this term:

Supervisor's signature - I give my permission for the student identified above to register for this project under my supervision:

Date: 19/08/11

Unit chair/director/designate's name:

Unit chair/director/designate's signature - I certify that this project conforms to departmental requirements for 396 courses: