rdf-syntax-grammar
mods:
  schema location: http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-2.xsd
  title info:
    title: Large-scale analysis of phylogenetic search behavior
  name:
    name part: Park, Hyun Jung.
    role:
      role term: creator
  name:
    name part: Williams, Tiffani L.
    role:
      role term: thesis advisor.
  type of resource: text
  genre: bibliography
  origin info:
    place:
      place term: txu
    date issued: 2010
    issuance: monographic
  language:
    language term: eng
  physical description:
    form: electronic
    form: remote
    extent: 1 online resource.
  abstract: Phylogenetic analysis is used in all branches of biology by inferring evolutionary trees. Applications include designing more effective drugs, tracing the transmission of deadly viruses, and guiding conservation and biodiversity efforts. Most analyses rely on effective heuristics for obtaining accurate trees. However, relatively little work has been done to analyze quantitatively the behavior of phylogenetic heuristics in tree space. This is important, because a better understanding of local search behavior can facilitate the design of better heuristics, which ultimately leads to more accurate depictions of the true evolutionary relationships. In order to access and analyze the tree search space, we implement an effective local search heuristic. Having an effective heuristic that can open the space is important, since no search heuristic in this field can effectively provide data collec- tion control. So we have implemented and estimated a search heuristic, Simple Local Search or SLS, that works reasonably well in the space. Our investigations led to several interesting observations about the behavior of a search heuristic and the tree search space. We studied the correlation of tree features of search path trees, where tree features refer to the parsimony score, the Robinson- Foulds distance and the homoplasy measure. Most importantly from the results, parsimony score was highly correlated with Robinson-Foulds distance only in trees that lie on the search path to a local optimum. We also note that the scores of neighborhoods along search paths improve together, as a local search progresses. Correlations of tree features of search path trees are particularly useful in characterizing and controlling a search path. This paper proposes one possible stopping criterion to maximize the tree search results while minimizing computational time tested on three biological datasets using the correlation between the parsimony score and the RF distance value of search path trees.…
  note: by Hyun Jung Park.
  note: "Major Subject: Computer Science"
  note: Title from author supplied metadata (automated record created 2010-03-12 12:08:51).
  note: Electronic resource.
  note: Master of Science Texas A&M University 2007 http://hdl.handle.net/1969.1/ETD-TAMU-1452
  note: Includes bibliographical references.
  note: Text (Thesis)
  subject:
    topic: Major computer science
  subject:
    topic: maximum parsimony
  subject:
    topic: phylogenetic trees
  identifier: http://hdl.handle.net/1969.1/ETD-TAMU-1452
  record info:
    record content source: TXA
    record creation date: 100426
    record change date: 20151201120103.0
    record identifier: in00002582165