WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Accelerating the neighbor-joining algorithm using the adaptive bucket data structure
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Large-scale neighbor-joining with NINJA
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
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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@hungry.com Supplementary information: http://bioinformatics.hungry.com/clearcut