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PubMed · 9385545

Numerical taxonomy on data: experimental results.

J Cohen·M Farach
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Abstract

We consider the problem of fitting an n x n distance matrix D by a tree metric T. This problem is NP-hard for most reasonable distance functions between D and T. Recently, an approximation algorithm was presented (Agarwala et al., 1996) which achieves a factor of 3 approximation to the L infinity best fitting tree. We call this method the Single Pivot (SP) heuristic. Within the biology community, the so-called Neighbor-Joining (NJ) heuristic (Saitou and Nei, 1987) has wide acceptance. In this paper, we introduced a new Double Pivot (DP) heuristic, which is an extension of the SP heuristic, and show that DP outperforms NJ on biological and random data.

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ClassificationComputational BiologyModels, TheoreticalNumerical Analysis, Computer-AssistedPhylogenyJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.

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J Cohen, M Farach. 1997. Numerical taxonomy on data: experimental results.. https://doi.org/10.1089/cmb.1997.4.547

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