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Bioinformatics. 2006 Nov 15;22(22):2823-4. Epub 2006 Sep 18.

Clearcut: a fast implementation of relaxed neighbor joining.

Author information

1
Department of Biological Sciences, University of Idaho, Moscow, ID, USA. sheneman@hungry.com

Abstract

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

PMID:
16982706
DOI:
10.1093/bioinformatics/btl478
[Indexed for MEDLINE]

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