Phylogenetics Syllabus and Reading Assignments

Phylogenetics Syllabus and Reading Assignments - Fall, 2013

The materials in the "Assigned Reading" column are directly related to the topics covered in class. Readings under "Additional Topics" are strictly optional and will not be covered on the exams.

Readings from:: Inferring Phylogenies Felsenstein, Sinauer Associates; 2 edition (September 4, 2003); Molecular Evolution: A Phylogenetic Approach. Page and Holmes, Wiley-Blackwell, 1st ed. (1998)

CLASS	DATE	TOPICS	ASSIGNED READING	ADDITIONAL TOPICS
1.	Aug. 27	Introduction to phylogenetics. Tree properties Lecture notes	Read: Page and Holmes Ch. 1 and 2 Understanding Evolutionary Trees Gregory, 2008. Review: You should already be familiar with the material on gene and genome organization in the first half of Ch. 3 of Page and Holmes. Look over pp 37-62 to make sure you know it. If not, read it carefully.	Felsenstein, Ch. 10: History and philosophy. Read: pp: 123-138.
2.	Aug. 29	Common ancestry, character states, evolutionary change on a tree. Lecture notes
3.	Sep. 3	Gene evolution I Lecture notes PS1 (due Sept. 12)	How Genomes Evolve, Genomes, T.A. Brown.
4.	Sep. 5	Gene evolution II Lecture notes		Origins, evolution and phenotypic impact of new genes, Kaessmann, Genome Research, 2010.
5.	Sep. 10	Multigene families, gene tree reconciliation Lecture notes PS2 (due Sept. 20)
6.	Sep. 12	Pieter: Introduction to phylogenetics software Test sequence file PS1 due Friday the 13th
7.	Sep. 17	Multigene families continued Lecture notes
8.	Sep. 19	Finding gene families in practise. Lecture notes PS2 due tomorrow at 3:30pm	Homology a personal view on some of the problems. Fitch, Trends Gen., 2000.	Distinguishing homologous from analogous proteins. Fitch, Syst. Zool., 1970.
9.	Sep. 24	Introduction to the practica Lecture notes
10.	Sep. 26	BLAST, sequence similarity searching. Lecture notes Prac 0: Introduction to Pyrrolysine: pdf, Practical assignment 0: pdf Worksheet docx	BLAST resources on line: Blast tutorial Using NCBI's BLAST BLAST documentation	Pyrrolysine review, Krzycki, 2011: pdf
11.	Oct. 1	More sequence similarity searching. Lecture notes
12.	Oct. 3	Even more sequence similarity searching! Lecture notes
13.	Oct. 8	In class Exam This exam is closed book. You may bring two pages (or one page, front and back) of your own notes.
14.	Oct. 10	Phylogeny reconstruction: maximum parsimony Lecture notes Counting trees	Page and Holmes Introduction to tree methods (6.1.0 - 6.1.3), pp. 172-178. Discrete methods (6.3) and Parsimony (6.4.0 - 6.4.3), pp. 187-191
15.	Oct. 15	Gene family review Lecture notes
16.	Oct. 17	Multiple sequence alignment Lecture notes
17.	Oct. 22	Multiple sequence alignment, Jalview demo Introductory slides	Multiple sequence alignment Pevsner, Ch. 6 Jalview reference card	Additional jalview info Jalview tutorial Screencast Other jalview documentation
18.	Oct. 24	Models of sequence evolution Lecture notes Prac 1: Practical assignment 1: pdf Worksheet: docx Data: pylB.fasta, species labels
19.	Oct. 29	Models of sequence evolution II Lecture notes
20.	Oct. 31	Maximum Likelihood Estimation Lecture notes	Read: Reading guide Kosiol et al. J. Biomed. Info., 2006. Page and Holmes 6.5: Maximum likelihood estimation Page and Holmes 5.3: Genetic distance	See pp. 454-458 of Sullivan and Joyce, 2005 for more information on the Akaike and Bayesian Information Criteria.
21.	Nov. 5	Tree inference by MLE Lecture notes PS3 (due Nov 13.)
22.	Nov. 7	Distance-based tree inference Lecture notes Prac 2: Practical assignment 2: pdf Worksheet: docx Data: fasta Taxonomy: txt	Page and Holmes, Distance based methods (6.2), pp. 179-186.
23.	Nov. 12	Distance-based tree inference, assessing phylogenetic accuracy Lecture notes	Page and Holmes, Comparing tree methods Bases for comparison (6.1.4), pp. 178 - 179. Pbs with distance methods (6.2.4), pp. 185 - 187. Parsimony, Likelihood (6.5.3, 6.5.4), pp. 199 - 201 Assessing tree quality Splits, section 6.6, pp. 201-208, but skip Box 6.5 True tree, section 6.7, pp. 209-216 Bootstrapping, section 6.8, but skip 6.83; pp. 216-222,225-227
24.	Nov. 14	Tree evaluation and interpretation Lecture notes
25.	Nov. 19	Reconciling and interpreting gene trees Lecture notes Notung 2.7, Example trees used in today's demo: zip
26.	Nov. 21	In class Exam This exam is closed book. You may bring two pages (or one page, front and back) of your own notes. Prac 3: Practical assignment 3: pdf Worksheet: docx Data: Prac3-speciestree.nwk, Prac3-genetree.nwk Readable species tree pdf, png.
27	Nov. 26	Class is cancelled Prac 3 due today at 5pm.
	Nov. 28	No class (Thanksgiving Holiday)
28.	Dec. 3	Project presentations I Reconciliation guide PS4 (due Dec. 6)
29.	Dec. 5	Project presentations II
FINAL	Dec. 12

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Last modified: November 19, 2013.
Maintained by Dannie Durand (durand@cs.cmu.edu).