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| Tutorial 1 | | Parameter Estimation by MLE |
tutorial01.ppt 266 KB
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| Notes: | - Maximum Likelihood Estimation
- Posterior Probability Estimator
- Prior Distributions |
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| Tutorial 2 | | Pairwise sequence alignment |
tutorial02.ppt 241 KB
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| Notes: | - Overlap alignment
- Dealing with affine gap scores |
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| Tutorial 3 | | More on Alignment |
tutorial03.ppt 206 KB
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| Notes: | - The "breaking number" problem
- Multiple-sequence alignment
- Approximation algorithm for min-cost multiple-sequence alignment |
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| Tutorial 4 | | Tree Alignments for Multiple Sequences |
tutorial04.ppt 228 KB
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| Notes: | -Clustal agorithm and profile alignment
-Lifted Tree Alignment |
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| Tutorial 6 | | Inference in HMMs |
tutorial06.ppt 427 KB
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| Notes: | - Inference queries: likelihood, most-probable state, and most-probable path.
- Dynamic programming algorithms: forward / backward / viterbi |
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| Tutorial 8 | | Baum-Welch Algorithm |
tutorial08.ppt 309 KB
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| Notes: | - Parameter estimation for HMMs
- Supervised vs. unsupervised learning
- The EM approach - Baum-Welch algorithm |
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| Tutorial 9 | | The EM algorithm for learning |
tutorial09.ppt 488 KB
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| Notes: | - using EM to find genotype statistics on the ABO locus |
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| Tutorial 10 | | Perfect Phylogeny |
tutorial10.ppt 437 KB
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| Notes: | - Efficient algorithm for the directed binary perfect phylogeny problem |
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| Tutorial 11 | | Parsimony |
tutorial11.ppt 289 KB
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| Notes: | - Sankoff's algorithm for weighted parsimony
- Fitch's algorithm as a special case of Sankoff's algorithm |
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| Tutorial 12 | | Distance Based Phylogenetic Reconstruction |
tutorial12.ppt 259 KB
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| Notes: | - The DLCA neighbor joining algorithm
- Atteson's robustness criteria
- Proof of robustness for DLCA |
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Technion - Israel Institute of Technology 
