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Clearcut: a fast implementation of relaxed neighbor joining
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(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:
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Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
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Metadata
- Authors
- Sheneman, L., Evans, J., & Foster, J. A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-09-18
- Volume
- 22
- Issue
- 22
- Pages
- 2823-2824
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2111802622
- Cited by
- 185
- References
- 2
- FWCI
- 1.96
- Type
- journal article
- Language
- en
- Open access
- closed
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