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Bioinformatics Advance Access originally published online on September 18, 2006
Bioinformatics 2006 22(22):2823-2824; doi:10.1093/bioinformatics/btl478
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Clearcut: a fast implementation of relaxed neighbor joining

Luke Sheneman *, Jason Evans and James A. Foster

Department of Biological Sciences, University of Idaho Moscow, ID, USA

*To whom correspondence should be addressed.

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(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: http://bioinformatics.hungry.com/clearcut

Contact: sheneman{at}hungry.com

Supplementary information: http://bioinformatics.hungry.com/clearcut

Received on June 8, 2006; revised on September 5, 2006; accepted on September 6, 2006

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