### Abstract

The number of the non-shared edges of two phylogenies is a basic measure of the distance (dissimilarity) between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the NNI distance. In this paper we give the first sub-quadratic time algorithm for finding the non-shared edges, which are then used to speed up the existing approximation algorithm for the NNI distance. The time is improved from O(n^{2}) to O(n log n). Another popular distance metric for phylogenies is the STT distance. Previous work on computing the STT distance focused on degree-3 trees only. We show that the STT distance can be applied in a broader sense, allowing us to cover degree-d trees, where d ≥ 3. In particular, we give a new approximation algorithm for the STT distance.

Original language | English (US) |
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Title of host publication | Algorithms and Computation - 11th International Conference, ISAAC 2000, Proceedings |

Editors | Shang-Hua Teng, D.T. Lee, Shang-Hua Teng |

Publisher | Springer Verlag |

Pages | 527-538 |

Number of pages | 12 |

ISBN (Print) | 3540412557, 9783540412557 |

State | Published - Jan 1 2000 |

Event | 11th Annual International Symposium on Algorithms and Computation, ISAAC 2000 - Taipei, Taiwan, Province of China Duration: Dec 18 2000 → Dec 20 2000 |

### 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 | 1969 |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Other

Other | 11th Annual International Symposium on Algorithms and Computation, ISAAC 2000 |
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Country | Taiwan, Province of China |

City | Taipei |

Period | 12/18/00 → 12/20/00 |

### Fingerprint

### ASJC Scopus subject areas

- Theoretical Computer Science
- Computer Science(all)

### Cite this

*Algorithms and Computation - 11th International Conference, ISAAC 2000, Proceedings*(pp. 527-538). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 1969). Springer Verlag.

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*Algorithms and Computation - 11th International Conference, ISAAC 2000, Proceedings.*Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 1969, Springer Verlag, pp. 527-538, 11th Annual International Symposium on Algorithms and Computation, ISAAC 2000, Taipei, Taiwan, Province of China, 12/18/00.

**Improved phylogeny comparisons : Non-shared edges, nearest neighbor interchanges, and subtree transfers.** / Hon, Wing Kai; Kao, Ming Yang; Lam, Tak Wah.

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

TY - GEN

T1 - Improved phylogeny comparisons

T2 - Non-shared edges, nearest neighbor interchanges, and subtree transfers

AU - Hon, Wing Kai

AU - Kao, Ming Yang

AU - Lam, Tak Wah

PY - 2000/1/1

Y1 - 2000/1/1

N2 - The number of the non-shared edges of two phylogenies is a basic measure of the distance (dissimilarity) between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the NNI distance. In this paper we give the first sub-quadratic time algorithm for finding the non-shared edges, which are then used to speed up the existing approximation algorithm for the NNI distance. The time is improved from O(n2) to O(n log n). Another popular distance metric for phylogenies is the STT distance. Previous work on computing the STT distance focused on degree-3 trees only. We show that the STT distance can be applied in a broader sense, allowing us to cover degree-d trees, where d ≥ 3. In particular, we give a new approximation algorithm for the STT distance.

AB - The number of the non-shared edges of two phylogenies is a basic measure of the distance (dissimilarity) between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the NNI distance. In this paper we give the first sub-quadratic time algorithm for finding the non-shared edges, which are then used to speed up the existing approximation algorithm for the NNI distance. The time is improved from O(n2) to O(n log n). Another popular distance metric for phylogenies is the STT distance. Previous work on computing the STT distance focused on degree-3 trees only. We show that the STT distance can be applied in a broader sense, allowing us to cover degree-d trees, where d ≥ 3. In particular, we give a new approximation algorithm for the STT distance.

UR - http://www.scopus.com/inward/record.url?scp=84949845409&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84949845409&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:84949845409

SN - 3540412557

SN - 9783540412557

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

SP - 527

EP - 538

BT - Algorithms and Computation - 11th International Conference, ISAAC 2000, Proceedings

A2 - Teng, Shang-Hua

A2 - Lee, D.T.

A2 - Teng, Shang-Hua

PB - Springer Verlag

ER -