schedules

Week	Day	Topic	Instructor	Assignments & lecture notes
23-Aug	Tu	Intro, syllabus, introductions	Thomas	Intro Slide Show
26-Aug	Th	Molecular Basis of Evolution and Codon Usage Bias	Thomas	Condon Usage Bias Slide Show

30-Aug	Tu	Evolutionary Change of Amino Acid Sequences	Thomas	Amino Acid Evolution Slide Show
1-Sep	Th	Computer lab (RM 205): amino acid substitional rates	Thomas

6-Sep	Tu	Evolutionary models for DNA sequence evolution	Thomas	DNA Evolution Slide Show
8-Sep	Th	Computer lab (RM 205): Nucleotide substitution rates	Thomas

13-Sep	Tu	Choosing among many models	Thomas	Model Selection Slide Show
15-Sep	Th	Computer lab (RM 205) About phylogenetics trees; intro to using PAUP		Data file - the COI gene in 10 Vert taxa (705bp)

20-Sep	Tu	Phylogenetic Inference: Distance based	Thomas	Trees and Distance Methods Slide Shows
22-Sep	Th	Phylogenetic Inference: Distance based	Thomas

27-Sep	Tu	Computer lab: distance approaches	Thomas	Data file - the 18S gene in 13 insect taxa (770bp) for Assignment 1
29-Sep	Th	Phylogenetic Inference: Maximum Parsimony	Thomas	Maximum Parsimony approach Slide Show

4-Oct	Tu	Computer lab: parsimony approaches	Thomas	Assignment 2
6-Oct	Th	Phylogenetic Inference: Maximum Likelihood	Thomas

11-Oct	Tu	Phylogenetic Inference: Maximum Likelihood	Thomas
13-Oct	Th	Computer lab: likelihood approaches		Assignment 3

18-Oct	Tu	Phylogenetic Inference: Bayesian Methods	Scot Kelchner
20-Oct	Th	Computer lab: Bayesian approaches	Thomas/ Kelchner	Data file - Strepsiptera nexus file with MrBayes block

25-Oct	Tu	Synonymous & nonsynonymous substitutions	Thomas
27-Oct	Th	GUEST: fates of duplicated genes	Deborah Johnson

1-Nov	Tu	Synonymous & nonsynonymous: case studies	Thomas
3-Nov	Th	Computer lab: dN/dS	Thomas	Assignment 4

8-Nov	Tu	GUEST: microbial phylogenetics	Mitch Day
10-Nov	Th	Accuracy & Statistical Tests: Phylogenetic Trees	Thomas

15-Nov	Tu	More accuracies and Statistical Tests	Thomas
17-Nov	Th	Computer lab: bootstrap, interior branch tests, and other assessments of the tree support (RM 205)	Thomas	Assignment 5

		Thanksgiving break…

29-Nov	Tu	Molecular Clocks and Linearized Trees	THomas
1-Dec	Th	Computer lab: linearized trees (RM 205)	Thomas	Assignment 6

6-Dec	Tu	GUEST: computational issues(?)	Luobin Yang
8-Dec	Th	GUEST: Poplation Trees from Genetic Markers	?	Final Exam assigned

TBA	TBA	Final Exam due: 5pm by email and hard copy