Graduate Bioinformatics: Molecular Systematics CBMG 688N/O
Syllabus Spring 2008 (with Tentative Lecture Schedule)
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Graduate Bioinformatics: Molecular Systematics CBMG 688N/O |
| CBMG 688N/O (combined) | ||||
| Topic | Comments | |||
M |
Jan. | 28 | ||
| W | 30 | Class will not meet | ||
| M | Feb. | 4 | Tree Searching Methods: Parsimony, Tree Search, NP Hard Problems |
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| W | 6 | Data sources: Gene Sequences, Genomes, SNPs, Sample genomes, Restriction site mapping, Molecular Evolution, gene families |
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| M | 11 |
Probability: Likelihood I, Markov Models, |
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| W | 13 | Models: Point Mutation, Rate Variation. |
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| M | 18 | |||
| W | 20 | Model-based methods (continued), Molecular Clocks & Calibration | ||
| M | 25 |
Alignment: ClustalX, Pileup, etc. |
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| W | 27 | Bayesian methods, Genetic Algorithms, Metropolis-Hastings, Monte Carlo | ||
| M | Mar. | 3 | Assessing Confidence; nonparametric bootstrapping, parametric bootstrapping | |
| W | 5 | Properties of Phylogenetic Methods and Performance of methods | ||
| M | 10 | Design of analysis & sources of error, part I: Base compositional bias, LogDet | ||
| W | 12 | Exam (Samples of old exams ) | ||
| How to present scientific information | ||||
| Molecular systematics at the population level | ||||
| CBMG 688O (only) | ||||
| Topic | Comments | |||
| M | 17 | Spring Break | ||
| W | 19 | Spring Break | ||
| M | 24 | Introduction to the term project | ||
| W | 26 | Tentative: Introduction, "Clone by wire", PAUP | Project proposal due | |
| M | 31 | Minisymposium I - Overview of project proposal | 1321a Symons Hall | |
| W | Apr. | 2 |
Minisymposium I - Overview of project proposal |
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| M | 7 | Work on projects | ||
| W | 9 | Work on projects | ||
| M | 14 | |||
| W | . | 16 | Tentative: PAUP II: Tree searching; Bootstrapping; Command line; Parameter Estimation | |
| M | 21 | Tentative: Molecular Methods in Environmental Microbiology | ||
| W | 23 |
Work on projects |
Project to reviewers | |
| M | 28 | Work on projects | ||
| W | 30 | Reviews due | ||
| M | May | 5 | Minisymposium II - Presentation of results | |
| W | 7 | Minisymposium II - Presentation of results | Term Projects Due | |
| M | 12 | Minisymposium II - Presentation of results | ||
| Orphan topics, to be covered if time permits | ||||
| Software: GCG II Phylip | ||||
| Review of DNA and PCR, Inconsistency of uncorrected methods | ||||
| Spectral methods, Lake's invariants, and Hadamard conjugation | ||||