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Clearcut: a fast implementation of relaxed neighbor joining
Ist Teil von
Bioinformatics, 2006-11, Vol.22 (22), p.2823-2824
Ort / Verlag
Oxford: Oxford University Press
Erscheinungsjahr
2006
Link zum Volltext
Quelle
MEDLINE
Beschreibungen/Notizen
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: