BIOL 4753-5753
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PART I: Phylogenetic Inference
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Week
DateLecture topicPractical topicNotes
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119-AugIntroduction to phylogenetics and tree thinking
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121-AugIntroduction to phylogenetics and tree thinking (cont.)
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226-AugIntroduction to phylogenetics and tree thinking (cont.)File formats and regular expressions (RegEx)
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228-Aug
Unix basics, remote access & running jobs in OSCER (by Dr. Henry Neeman)
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32-SepNo class - Labor Day HolidayNo class - Labor Day Holiday
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34-SepTree space & optimality criteria
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49-SepTree space & optimality criteria
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411-SepDistance methods
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516-SepModels of molecular evolution
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518-SepMultiple sequence alignmentMultiple sequence alignment
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623-SepMaximum likelihood, bootstrap & hypothesis testingML (RAXML) & bootstrap
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625-SepMaximum likelihood, bootstrap & hypothesis testing
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730-SepModels selection; rate heterogeneityRate heterogeneity: PartitionFinder
Deadline to submit outline for final project
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72-OctBayesian inferenceBayesian inference and ML
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87-OctMolecular clocksMolecular clocks - BEAST tutorial
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89-OctGene trees & species treesGene trees & species trees inference
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914-OctMidterm exam (phylogenetic inference)
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916-OctMidterm exam (cont.)
Due Sunday October 20 (11:59 pm)
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1021-OctTree networks & reticulation. PhylogenomicsGenome-scale gene tree & species tree inference
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PART II: Phylogenetic Comparative Methods
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1023-OctPhylogeography. Inferring biogeographic history using phylogenies
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1128-Oct
R basics. Introduction to reading, writing, manipulating, and visualizing trees in R
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1130-OctIntroduction to the phylogenetic comparative methodPhylogenetically independent contrasts in R
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124-NovBrownian motion and phylogenetically independent contrasts
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126-NovOther models of continuous trait evolution on treesFitting models of continuous trait evolution
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1311-NovAncestral state reconstruction of continuous and discrete traits
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1313-NovAncestral state reconstruction of continuous and discrete traits
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1418-NovEstimating speciation and extinction rates using phylogenies
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1420-NovFitting state-dependent diversification models in R using diversitree
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1525-NovStudent presentations - 3 sessions (3 classes in 1)3:00 to 7:00 pm
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1527-NovNo class - ThanksgivingNo class - Thanksgiving
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162-DecMoved to 25th Nov.
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164-DecMoved to 25th Nov.
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179-DecMoved to 25th Nov.
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1713-Dec
Deadline to submit term paper (11:59 pm)
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