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Biology 545 - Principles of Systematic Biology
Syllabus
Readings
Lecture 1 - Introduction & The Importance of Systematics: Notes Slides.
Lecture 2 - The History of Phylogenetics: Notes Slides.
Lecture 3 - Characters: Homology, Morphology: Notes Slides.
Lecture 4 - Characters: Molecular: Notes Slides.
Lecture 5 - Alignment Notes Slides.
Lecture 6A - Trees and Optimality Criteria: Parsimony: Notes Slides.
Lecture 6B - Optimality Criteria: ML & ME: Notes Slides.
Lecture 7 - Algorithmic Approaches: Notes Slides.
Lecture 8 - Searching Tree Space: Notes Slides.
Lecture 9 - The Importance of Models: Notes Slides.
Lecture 10 - Substitution Models: Notes Slides.
Lecture 11 - Increasing Model Complexity: Notes Slides.
Lecture 12 - Model Selection: Notes Slides.
Lecture 13 - Method Performance: Notes Slides.
Lecture 14 - Support: Consensus, Decay & Bootstrap: Notes Slides.
Lecture 15 - Support: Jackknife & Bayesian Nodal Probabilities: Notes Slides.
Lecture 16 - Hypothesis Testing: Notes Slides.
Lecture 17 - Molecular Clocks: Notes Slides.
Lecture 18 - Multiple Data Sets: Supermatrices, Supertrees, Partitions and Mixtures Notes Slides.
Lecture 19 - Species-Tree Estimation: Notes Slides.
Lecture 20 - Taxon Sampling: Notes Slides.
Lab 1 - Coding Morphology & Intro to Unix.
Lab 2 - Alignment.
Data set.
Lab 3 - Parsimony & PAUP*
Data Set
Lab 4 - Maximum Likelihood, GARLi & BEAST
Config File for GARLi
Lab 5 - Assessing Nodal Support
Problem Set 1 Answers
Old Exam 1
Problem Set 2 Answers
Old Exam 2
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