Spring 2017
(Fall 2010 offering,Spring 2016 offering)

[Staff] [Discussion Forum] [Information] [Materials]


. Name Email address Office hours
Instructor Luay K. Nakhleh by appointment, DH 3119
Teaching Assistant Leo Elworth by appointment, DH 3121

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Discussion Forum

We will be using Piazza for discussions. Feel free to post questions and responses about the material covered in the lecture, homework problems, etc. However, please do not give any information that relates to your own solution for a homework problem. To go to the discussion forum, click here.
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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 Materials
1 Administrivia and background material Slides (full), Slides (handout) syllabus
2 Sequence alignment: General overview Slides (full), Slides (handout)
3 Sequence alignment: Scoring schemes Slides (full), Slides (handout)
4 Sequence alignment: Dynamic programming algorithms for pairwise alignment Slides (full), Slides (handout)
5 Significance of estimated sequence alignments Slides (full), Slides (handout)
6 Markov chains and hidden Markov models Slides (full), Slides (handout) homework 1 (due Feb 7)
7 Pairwise HMMs and sequence alignment Slides (full), Slides (handout) homework 2 (due Feb 21)
8 Profiles and multiple sequence alignments Slides (full), Slides (handout)
9 Phylogenetics: Recovering Evolutionary History Slides (full), Slides (handout)
10 Phylogenetics: Building Phylogenetic Trees Slides (full), Slides (handout)
11 Phylogenetics: Parsimony Slides (full), Slides (handout) homework 3 (due Apr 6)
12 Phylogenetics: Distance-based Methods Slides (full), Slides (handout) homework 4 (due Apr 18)
13 Phylogenetics: Likelihood Slides (full), Slides (handout)
14 Phylogenetics: Bayesian Inference Slides (full), Slides (handout)

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