Scribe: J. Zwolak

Today's Handouts and Announcements

• No handouts.

Today's Topics

• Phylogenetic trees were discussed. Some of the basics of the biological side are:

  • There are two different types of characteristics of organisms to look at: molecular and physical.

  • Clade - a group of species which share a common ancestor with each other and only each other. They appear in the tree as sub trees (not all sub trees are clades).

  • There are also species trees which are similar to phylogenetic trees in that both can use the same methods to be generated. However, phylogenetic trees are more detailed.

• Means to generate phylogenetic trees:

  • Parsimony

  • Maximum likelihood

  • Distance matrix

  • Methods of invariants

• Parsimony - the most parsimonious tree is the one in which the least number of changes occur.

• Phylogenies that are not perfect create an NP-hard problem when one tries to find the best phylogenetic tree.

Today's Sources

• Setubal and Meidanis: Chapter 6.

• Salzberg, Searls, and Kasif: None.

• Joseph Felsenstein
  Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach
  Journal of Molecular Evolution 17, 1981, 368-376.

• Junhyong Kim and Tandy Warnow
  Tutorial on Phylogenetic Tree Estimation
  Tutorial for ISMB 99.