Clearcut: a fast implementation of relaxed neighbor joining

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(N3) time complexity, where N represents the number of taxa in the inpu...

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Vydáno v:Bioinformatics Ročník 22; číslo 22; s. 2823 - 2824
Hlavní autoři: Sheneman, Luke, Evans, Jason, Foster, James A.
Médium: Journal Article
Jazyk:angličtina
Vydáno: Oxford Oxford University Press 15.11.2006
Oxford Publishing Limited (England)
Témata:
Algorithms
Bioinformatics
Biological and medical sciences
Clearcutting
Computational Biology - methods
Computer Simulation
Evolution, Molecular
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Models, Genetic
Models, Statistical
Phylogeny
Programming Languages
Software
Phylogenetic tree
Bootstrap
C language
Bioinformatics
Algorithm
Scope note
Velocity
Distance
Optimization
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
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Popis
Shrnutí: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(N3) 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 N2logN 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: Contact:sheneman@hungry.com Supplementary information:
Bibliografie:To whom correspondence should be addressed.
Associate Editor: Keith A Crandall
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ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btl478