Minimizing phylogenetic number to find good evolutionary trees

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Inferring phylogenetic trees is a fundamental problem in computational-biology. We present a new objective criterion, the phylogenetic number, for evaluating evolutionary trees for species defined by biomolecular sequences or other qualitative characters. The phylogenetic number of a tree T is the maximum number of times that any given character state arises in T. By contrast, the classical parsimony criterion measures the total number of times that different character states arise in T. We consider the following related problems: finding the tree with minimum phylogenetic number, and computing the phylogenetic number of a given topology in which only the leaves are ... continued below

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26 p.

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Goldberg, L. A.; Goldberg, P. W.; Phillips, C. A.; Sweedyk, E. & Warnow, T. May 1995.

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  • Sandia National Laboratories
    Publisher Info: Sandia National Labs., Albuquerque, NM (United States)
    Place of Publication: Albuquerque, New Mexico

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Description

Inferring phylogenetic trees is a fundamental problem in computational-biology. We present a new objective criterion, the phylogenetic number, for evaluating evolutionary trees for species defined by biomolecular sequences or other qualitative characters. The phylogenetic number of a tree T is the maximum number of times that any given character state arises in T. By contrast, the classical parsimony criterion measures the total number of times that different character states arise in T. We consider the following related problems: finding the tree with minimum phylogenetic number, and computing the phylogenetic number of a given topology in which only the leaves are labeled by species. When the number of states is bounded (as is the case for biomolecular sequence characters), we can solve the second problem in polynomial time. We can also compute a fixed-topology 2-phylogeny (when one exists) for an arbitrary number of states. This algorithm can be used to further distinguish trees that are equal under parsimony. We also consider a number of other related problems.

Physical Description

26 p.

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OSTI as DE95011893

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  • 1995 symposium on combinatorial pattern matching, Helsinki (Finland), 4-7 Jul 1995

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  • Other: DE95011893
  • Report No.: SAND--95-0831C
  • Report No.: CONF-9507123--1
  • Grant Number: AC04-94AL85000
  • Office of Scientific & Technical Information Report Number: 70782
  • Archival Resource Key: ark:/67531/metadc706960

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  • May 1995

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  • Sept. 12, 2015, 6:31 a.m.

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  • Feb. 15, 2016, 4:21 p.m.

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Goldberg, L. A.; Goldberg, P. W.; Phillips, C. A.; Sweedyk, E. & Warnow, T. Minimizing phylogenetic number to find good evolutionary trees, article, May 1995; Albuquerque, New Mexico. (digital.library.unt.edu/ark:/67531/metadc706960/: accessed October 22, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.