### Abstract

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 parsimonycriterion 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.

Original language | English (US) |
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Title of host publication | Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings |

Editors | Zvi Galil, Esko Ukkonen |

Publisher | Springer-Verlag |

Pages | 102-127 |

Number of pages | 26 |

ISBN (Print) | 3540600442, 9783540600442 |

DOIs | |

State | Published - Jan 1 1995 |

Event | 6th Annual Symposium on Combinatorial Pattern Matching, CPM 1995 - Espoo, Finland Duration: Jul 5 1995 → Jul 7 1995 |

### Publication series

Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
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Volume | 937 |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Other

Other | 6th Annual Symposium on Combinatorial Pattern Matching, CPM 1995 |
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Country | Finland |

City | Espoo |

Period | 7/5/95 → 7/7/95 |

### Fingerprint

### ASJC Scopus subject areas

- Theoretical Computer Science
- Computer Science(all)

### Cite this

*Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings*(pp. 102-127). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 937). Springer-Verlag. https://doi.org/10.1007/3-540-60044-2_38

**Minimizing phylogenetic number to find good evolutionary trees.** / Goldberg, Leslie Ann; Goldberg, Paul W.; Phillips, Cynthia A.; Sweedyk, Elizabeth; Warnow, Tandy.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

*Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings.*Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 937, Springer-Verlag, pp. 102-127, 6th Annual Symposium on Combinatorial Pattern Matching, CPM 1995, Espoo, Finland, 7/5/95. https://doi.org/10.1007/3-540-60044-2_38

}

TY - GEN

T1 - Minimizing phylogenetic number to find good evolutionary trees

AU - Goldberg, Leslie Ann

AU - Goldberg, Paul W.

AU - Phillips, Cynthia A.

AU - Sweedyk, Elizabeth

AU - Warnow, Tandy

PY - 1995/1/1

Y1 - 1995/1/1

N2 - 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 parsimonycriterion 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.

AB - 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 parsimonycriterion 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.

UR - http://www.scopus.com/inward/record.url?scp=84957868373&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84957868373&partnerID=8YFLogxK

U2 - 10.1007/3-540-60044-2_38

DO - 10.1007/3-540-60044-2_38

M3 - Conference contribution

AN - SCOPUS:84957868373

SN - 3540600442

SN - 9783540600442

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 102

EP - 127

BT - Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings

A2 - Galil, Zvi

A2 - Ukkonen, Esko

PB - Springer-Verlag

ER -