Lecture 30: Maximum Parsimony and minimum mutation methods -

Fundamental Algorithms in Bioinformatics

Lecture 30: Maximum Parsimony and minimum mutation methods

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Building evolutionary trees from sequence data. The Maximum Parsimony criteria, the special case of Perfect Phylogeny, and the Fitch-Hartigon dynamic program to minimize mutations when the tree and a sequence alignment are known.

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Postscript: Where to go next

Some suggestions of where the student can get more exposure to algorithms for bioinformatics and computational biology.

Published 02/01/10

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 values and their misuse.

Published 01/30/10

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 molecular clock.

Published 01/29/10