The performance of phylogenetic methods on trees of bounded diameter

Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We study the convergence rates of neighbor-joining and several new phylogenetic reconstruction methods on families of trees of bounded diameter. Our study presents theoretically obtained convergence rates, as well as an empirical study based upon simulation of evolution on random birth-death trees. We find that the new phylogenetic methods offer an advantage over the neighborjoining method, except at low rates of evolution where they have comparable performance. The improvement in performance of the new methods over neighborjoining increases with the number of taxa and the rate of evolution.

Original languageEnglish (US)
Title of host publicationAlgorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings
EditorsBernard M. E. Moret, Olivier Gascuel
PublisherSpringer-Verlag
Pages214-226
Number of pages13
ISBN (Print)3540425160
DOIs
StatePublished - Jan 1 2001
Externally publishedYes
Event1st International Workshop on Algorithms in Bioinformatics, WABI 2001 - Arhus, Denmark
Duration: Aug 28 2001Aug 31 2001

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume2149
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other1st International Workshop on Algorithms in Bioinformatics, WABI 2001
CountryDenmark
CityArhus
Period8/28/018/31/01

Fingerprint

Phylogenetics
Joining
Empirical Study
Convergence Rate
Rate of Convergence
Simulation

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Nakhleh, L., Roshan, U., St. John, K., Sun, J., & Warnow, T. (2001). The performance of phylogenetic methods on trees of bounded diameter. In B. M. E. Moret, & O. Gascuel (Eds.), Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings (pp. 214-226). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2149). Springer-Verlag. https://doi.org/10.1007/3-540-44696-6_17

The performance of phylogenetic methods on trees of bounded diameter. / Nakhleh, Luay; Roshan, Usman; St. John, Katherine; Sun, Jerry; Warnow, Tandy.

Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. ed. / Bernard M. E. Moret; Olivier Gascuel. Springer-Verlag, 2001. p. 214-226 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2149).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Nakhleh, L, Roshan, U, St. John, K, Sun, J & Warnow, T 2001, The performance of phylogenetic methods on trees of bounded diameter. in BME Moret & O Gascuel (eds), Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2149, Springer-Verlag, pp. 214-226, 1st International Workshop on Algorithms in Bioinformatics, WABI 2001, Arhus, Denmark, 8/28/01. https://doi.org/10.1007/3-540-44696-6_17
Nakhleh L, Roshan U, St. John K, Sun J, Warnow T. The performance of phylogenetic methods on trees of bounded diameter. In Moret BME, Gascuel O, editors, Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. Springer-Verlag. 2001. p. 214-226. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/3-540-44696-6_17
Nakhleh, Luay ; Roshan, Usman ; St. John, Katherine ; Sun, Jerry ; Warnow, Tandy. / The performance of phylogenetic methods on trees of bounded diameter. Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. editor / Bernard M. E. Moret ; Olivier Gascuel. Springer-Verlag, 2001. pp. 214-226 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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