Postscript: Where to go next
Postscript: Where to go next
Some suggestions of where the student can get moreexposure to algorithms for bioinformatics and computational biology.
1 Feb 2010
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1min
Lecture 30: Maximum Parsimony and minimum mutation methods
Lecture 30: Maximum Parsimony and minimum mutation methods
Building evolutionary trees from sequence data. The Maximum Parsimony criteria, the special case of Perfect Phylogeny, a... Read more
31 Jan 2010
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3mins
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Lecture 29; Additive trees and the Neighbor-Joining algorithm
Lecture 29; Additive trees and the Neighbor-Joining algorithm
Additive trees and their construction. The Neighbor-Joining algorithm and its use with near-additive data. Bootstrap va... Read more
30 Jan 2010
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3mins
Lecture 28: Algorithms for Ultrametric trees — molecular clocks
Lecture 28: Algorithms for Ultrametric trees — molecular clocks
Algorithms for constructing an Ultrametric Tree from an Ultrametric Matrix, and the relationship of ultrametrics to the ... Read more
29 Jan 2010
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3mins
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Lecture 27: Introduction to evolutionary trees - Ultrametric trees
Lecture 27: Introduction to evolutionary trees - Ultrametric trees
lntroduction to trees that represent evolution. We start with the case of perfect data: the Ultrametric tree case.
28 Jan 2010
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1min
Lecture 26: Hidden Markov models - The Backwards algorithm
Lecture 26: Hidden Markov models - The Backwards algorithm
What the Backwards algorithm computes and why we want it.Profile HMMs and their use. Cleaning up some topics in sequence... Read more
27 Jan 2010
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2mins
Lecture 25: From the Vitterbi algorithm to the forward algorithm
Lecture 25: From the Vitterbi algorithm to the forward algorithm
This class finishes the discussion of the Vitterbi algorithm, its time analysis and the traceback algorithm. Introductio... Read more
26 Jan 2010
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3mins
Lecture 24: Hidden Markov models and the Vitterbi algorithm
Lecture 24: Hidden Markov models and the Vitterbi algorithm
Finish the discussion of HMMs for CpG islands. Introductionto the Vitterbi algorithm (really dynamic programming)to find... Read more
25 Jan 2010
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4mins
Lecture 23: Hidden Markov models
Lecture 23: Hidden Markov models
Hidden Markov models to identify CpG islands. Thislecture follows the discussion in Durbin and Eddy.
24 Jan 2010
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4mins
Lecture 22: From profiles to Markov models
Lecture 22: From profiles to Markov models
Finish the discussion of profiles and log-odds ratios. introduction to Markov Modelsand Hidden Markov Models
23 Jan 2010
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4mins
