Spring 2014
(For Fall 2010 offering, which was focused mostly on population genetics, click here.)

[Staff] [Information] [Materials]


. Name Email address Office hours
Instructor Luay K. Nakhleh by appointment, DH 3119
Teaching Assistant Xian Fan by appointment, DH 3075
Teaching Assistant Dingqiao Wen by appointment, DH 3117

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Course Information

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Course Material

Course material (homework assignments, schedule of topics, slides, etc.) will be posted in this section.

Slides Set # Topic Slides Homework assignments
1 Administrivia and background material PDF
2 Sequence alignment: General overview PDF
3 Sequence alignment: Scoring schemes PDF
4 Sequence alignment: Dynamic programming algorithms for pairwise alignment PDF
5 Significance of estimated sequence alignments PDF
6 Markov chains and hidden Markov models PDF homework 1
7 Pairwise HMMs and sequence alignment PDF
8 Profiles and multiple sequence alignments PDF homework 2
9 Phylogenetics: Recovering Evolutionary History PDF
10 Phylogenetics: Building Phylogenetic Trees PDF
11 Phylogenetics: Distance-based Methods PDF
12 Phylogenetics: Sequence-based Methods PDF
13 Phylogenetics: Bayesian Analysis PDF homework 3
14 Phylogenomics PDF
15 Genome characteristics and annotation PDF homework 4

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