Phylogenetics Syllabus and Reading Assignments - Fall, Mini-2 2011

The materials in the "Assigned Reading" column are directly related to the topics covered in class. Readings under "Additional Topics" are strictly optional and will not be covered on the exams.

Readings from:
Inferring Phylogenies Felsenstein, Sinauer Associates; 2 edition (September 4, 2003)
Molecular Evolution: A Phylogenetic Approach. Page and Holmes, Wiley-Blackwell, 1st ed. (1998)

CLASS
DATE
TOPICS
ASSIGNED READING
ADDITIONAL TOPICS
1. Oct. 25 Introduction to phylogenetics. Tree properties
lecture notes
Page and Holmes
Read Chapters 1 and 2
Review Chapter 3: pp 31-62.
Felsenstein
Chapter 10: History and philosophy. Read: pp: 123-138.
 
2. Oct. 27 More introduction to phylogenetics.
lecture notes

 Understanding Evolutionary Trees
Gregory, 2008.
Page and Holmes
Read Chapter 3: pp. 63-87.
 
3. Nov. 1 Multiple Sequence alignment
lecture notes

Problem set 1 		   
4. Nov. 3 Models of DNA substitution.
lecture notes

Practicum 1
Multiple sequence alignment
Pevsner, Ch. 6
Procteret al., Visualization of multiple alignments, phylogenies and gene family evolution, 2010.
Models of substitution
Page and Holmes, Chapter 5.
 
5. Nov. 8 Parsimony; traversing tree space. Lecture notes

Projects

Problem set 1 due in class.
Page and Holmes,
Introduction to tree methods (6.1.0 - 6.1.3), pp. 172-178.
Discrete methods (6.3) and Parsimony (6.4.0 - 6.4.3), pp. 187-191
 
6. Nov. 10 Distance based methods Lecture notes
Page and Holmes,
Distance based methods (6.2.0-6.2.3), pp. 179-185.
 
7. Nov. 15 Maximum likelihood estimation Lecture notes

Homework 2
Page and Holmes,
Maximum likelihood (6.5.0-6.5.2), pp. 183 - 196.
  
8. Nov. 17 Model selection Lecture notes

    
9. Nov. 22
Practicum 2 		   
  Nov. 24 No class (Thanksgiving Holiday)    
10. Nov. 29 Validating your tree. What can go wrong? Lecture notes

Practicum 3
Page and Holmes, Comparing tree methods
Bases for comparison (6.1.4), pp. 178 - 179.
Pbs with distance methods (6.2.4), pp. 185 - 187.
Parsimony, Likehihood (6.5.3, 6.5.4), pp. 199 - 201
 
11. Dec. 1 Gene Duplication
  Lecture notes

    
12. Dec. 6 Horizontal Gene Transfer
  Lecture notes

    
13. Dec. 8 Species trees, phylogenomics;
  Lecture notes

    
  Dec. 16   Final Exam:   5:30pm - 8:30pm,   Location TBA
 This exam is closed book. You may bring two pages (or one page, front and back) of your own notes.  


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Last modified: Nov. 2, 2011.
Maintained by Dannie Durand (durand@cs.cmu.edu).