The performance of phylogenetic methods on trees of bounded diameter

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

doi:10.1007/3-540-44696-6_17

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 proceeding › Conference contribution

6 Scopus citations

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 language	English (US)
Title of host publication	Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings
Editors	Bernard M. E. Moret, Olivier Gascuel
Publisher	Springer Verlag
Pages	214-226
Number of pages	13
ISBN (Print)	3540425160
DOIs	https://doi.org/10.1007/3-540-44696-6_17
State	Published - 2001
Externally published	Yes
Event	1st International Workshop on Algorithms in Bioinformatics, WABI 2001 - Arhus, Denmark Duration: Aug 28 2001 → Aug 31 2001

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	2149
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	1st International Workshop on Algorithms in Bioinformatics, WABI 2001
Country/Territory	Denmark
City	Arhus
Period	8/28/01 → 8/31/01

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/3-540-44696-6_17

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

Nakhleh, Luay ; Roshan, Usman ; St. John, Katherine et al. / 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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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.",

author = "Luay Nakhleh and Usman Roshan and {St. John}, Katherine and Jerry Sun and Tandy Warnow",

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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

The performance of phylogenetic methods on trees of bounded diameter. / Nakhleh, Luay; Roshan, Usman; St. John, Katherine et al.
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 proceeding › Conference contribution

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AB - 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.

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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)). doi: 10.1007/3-540-44696-6_17

The performance of phylogenetic methods on trees of bounded diameter

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