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Graduate Bioinformatics: Molecular Systematics CBMG 688N/O
Syllabus Spring 2010 (with Tentative Lecture Schedule)
CBMG 688N/O (combined)  
      Topic Comments

M

 Jan. 25

Lecture: Mechanics, Introduction, phylogenetic information, overview

 
W   27 Lecture: Sequencing technologies  
M Feb. 1

Lecture: Tree Searching Methods: Parsimony, Tree Search, NP Hard Problems

 
W   3

Snow

  
M   8

Snow

  
W   10

Snow

  
M   15 Lecture: Probability: Likelihood I, Markov Models, Point Mutation, Rate Variation.  
W   17 Lecture: Multiple Sequence Alignment  
M   22

Projects

  
W   24 Projects  
M Mar. 1 Lecture: Implementing likelihood: DNAml, fastDNAml, raxML Homework 1
W   3 Projects  
M   8 Lecture: Bayesian methods, Genetic Algorithms, Metropolis-Hastings, Monte Carlo Intro to term projects
W   10 Lecture: Assessing Confidence; nonparametric bootstrapping, parametric bootstrapping Homework 2
M   15 Spring Break  
W   17 Spring Break  
M   22 the presentation of scientific information Project proposal due
W   24 Projects  
M   29 Minisymposium I - Overview of project proposal 1321a Symons Hall
W   31

Minisymposium I - Overview of project proposal

  
M Apr. 5 Lecture: Distance Methods  
W   7 Lecture: More complex models, LogDet, Heterotachy Homework 3
M   12

Lecture: Hypothesis testing

  
W . 14 Projects  
M   19 Projects  
W   21

Exam (Samples of old exams )

Project to reviewers
M   26 Projects  
W   28 Minisymposium II - Presentation of results Reviews due
M May 3 Minisymposium II - Presentation of results  
W   5 Projects Term Projects Due
M   10    
Orphan topics, to be covered if time permits
      Software: GCG II Phylip  
      Review of DNA and PCR, Inconsistency of uncorrected methods  
      Spectral methods, Lake's invariants, and Hadamard conjugation  

Legacy syllabus: Fall 2008