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Why Neighbor-Joining Works

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Abstract

We show that the neighbor-joining algorithm is a robust quartet method for constructing trees from distances. This leads to a new performance guarantee that contains Atteson’s optimal radius bound as a special case and explains many cases where neighbor-joining is successful even when Atteson’s criterion is not satisfied. We also provide a proof for Atteson’s conjecture on the optimal edge radius of the neighbor-joining algorithm. The strong performance guarantees we provide also hold for the quadratic time fast neighbor-joining algorithm, thus providing a theoretical basis for inferring very large phylogenies with neighbor-joining.

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Authors and Affiliations

  1. Department of Mathematics and Computer Science, UC Berkeley, 970 Evans Hall, Berkeley, CA, 94720, USA

    Radu Mihaescu, Dan Levy & Lior Pachter

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  1. Radu Mihaescu
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  2. Dan Levy
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  3. Lior Pachter
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Correspondence to Lior Pachter.

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Mihaescu, R., Levy, D. & Pachter, L. Why Neighbor-Joining Works. Algorithmica 54, 1–24 (2009). https://doi.org/10.1007/s00453-007-9116-4

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  • DOI: https://doi.org/10.1007/s00453-007-9116-4

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