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Molecular Systematics

Molecular Systematics and Evolution (ZOOL 6305) - Syllabus

Fall 2015 Lecture notes, etc. (NOTE: All information on this page is a work in progress and may change at any time)

Part 1 - Theory and Background (David Ray)

Unit 1 - Introduction & Tree Thinking - Powerpoint

     Tree thinking quiz, answers

Unit 2 - Molecular Evolution and Data - Powerpoint

Unit 3 - Taxonomic Units - Powerpoint

Unit 4 - Sequence Alignment - Powerpoint

Unit 5 - Intro to Tree Inference & Models of DNA Evolution - Powerpoint

Unit 6 - Clustering Methods - Powerpoint

Unit 7 - Maximum Likelihood - Powerpoint

Unit 8 - Bayesian Analysis - Powerpoint

Unit 9 - Parsimony - Powerpoint

Unit 10 - Tree Confidence and Support - Powerpoint

Unit 11 - Whole Genome Phylogenetics - Powerpoint

Part 2 - Practical Application (Neal Platt)

Unit 12 - Introduction to the CLI, Data Formats, & Troubleshooting - pdf, notes

Unit 13 - Obtaining Data & Sequence Alignment - notes

Unit 14 - Substitution Models - notes

Unit 15/16 - Distance Methods/Parsimony - notes

Unit 17 - Maximum Likelihood - notes

Unit 18 - Bayesian Methods - notes

Unit 19 - Hypothesis Testing & Ancestral Rate Reconstruction - notes