Clearcut: a fast implementation of relaxed neighbor joining.

Clearcut: a fast implementation of relaxed neighbor joining. Research Abstract Details 

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Clearcut: a fast implementation of relaxed neighbor joining. Abstract Text:

Luke Sheneman,Jason Evans,James A Foster,

SUMMARY: Clearcut is an open source implementation for the relaxed neighbor joining (RNJ) algorithm. While traditional neighbor joining (NJ) remains a popular method for distance-based phylogenetic tree reconstruction, it suffers from a O(N(3)) time complexity, where N represents the number of taxa in the input. Due to this steep asymptotic time complexity, NJ cannot reasonably handle very large datasets. In contrast, RNJ realizes a typical-case time complexity on the order of N(2)logN without any significant qualitative difference in output. RNJ is particularly useful when inferring a very large tree or a large number of trees. In addition, RNJ retains the desirable property that it will always reconstruct the true tree given a matrix of additive pairwise distances. Clearcut implements RNJ as a C program, which takes either a set of aligned sequences or a pre-computed distance matrix as input and produces a phylogenetic tree. Alternatively, Clearcut can reconstruct phylogenies using an extremely fast standard NJ implementation. AVAILABILITY: Clearcut source code is available for download at: http://bioinformatics.hungry.com/clearcut

Clearcut: a fast implementation of relaxed neighbor joining. Publishing Authors By Initials

L Sheneman,J Evans,JA Foster,

For similar information science: computing methodologies: software research abstracts see: information science: computing methodologies: software research

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Clearcut: a fast implementation of relaxed neighbor joining. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Bioinformatics (Oxford, England)

VOLUME: 22

Page Numbers: 2823-4

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 18

MONTH: 09

YEAR: 2006

Clearcut: a fast implementation of relaxed neighbor joining. Information

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LANGUAGE: eng

NlmUniqueID: 9808944

Clearcut: a fast implementation of relaxed neighbor joining. Keywords Mesh Terms:

KEYWORDS: Software

MESH TERMS: methods

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Grant and Affiliation Information for Clearcut: a fast implementation of relaxed neighbor joining.

AFFILIATION: Department of Biological Sciences, University of Idaho, Moscow, ID, USA. sheneman@hungry.com

Country: England

AGENCY: United States NCRR

GRANT: P20 RR16454

ACRONYM: RR

MEDLINETA: Bioinformatics

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