Date

Topic

Reading

Wed, Jan 21

Intro. And Overview

Graphs: Pev 247-60

Mol. Biol: Pev. 57-78

Shamir:

http://www.cs.tau.ac.il/~rshamir/ge/07/scribe/lec01.pdf

Shamir Notes (8.1.1-8.1.2):

http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf

Mon, Jan 26

Parsimony & Dynamic Programming: Sankoff & Fitch

Fel: Ch1-3, 6.

Shamir Notes (8.2.2-8.2.7):

http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf

Wed, Jan 28

Parsimony 2:

Perfect Phylogeny & Compatibility

Fel: Ch8

Shamir notes: (8.2.9)

Mon, Feb 2

Distances:

Additive & Quartets

UPGMA & Ultrametric

Pev. 358-367

Fel: Ch11(pp. 161-166) Ch12 (pp. 176-178)

Wed, Feb 4

Distances: Neighbor Joining

Fel: Ch11 (pp. 166-170)

Mon, Feb 9

Models of DNA evolution & Markov Chains

Fel: Ch11 (p. 155-159)

Ch13 (pp. 196-200)

Wed, Feb 11

Likelihood

Fel: Ch16 (pp. 248-260)

Mon, Feb 16

HOLIDAY

Wed, Feb 18

Branch length estimation.

Tree Space and Searching

Splits metric.

EM Branch length notes

Fel: Ch4-5

Ch30 (pp. 528-534)

Mon, Feb 23

Branch swapping (NNI, SPR, TBR)

Bayesian estimates and MCMC.

Consensus Trees (Strict and Majority)

Fel:

Ch30 (pp. 521-524)

Ch18 (pp. 288-296)

Wed, Feb 25

Bootstrapping Trees. Supertrees. Aho's algorithm.

Ch12 (pp. 189-191)

Fel: Ch20 (pp. 335-342)

Mon, Mar 2

Whole-genome Phylogeny.

Gene Trees and Species Trees.

Fel: Ch29 (pp. 509-519)

*NEW*: Eddy algorithm paper

Wed, Mar 4

NO CLASS

Pev. 125-138

Shamir: http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe10/lec10.ps.gz