Abstract
We present a new distance based quartet method for phylogenetic tree reconstruction, called Minimum Tree Cost Quartet Puzzling. Starting from a distance matrix computed from natural data, the algorithm incrementally constructs a tree by adding one taxon at a time to the intermediary tree using a cost function based on the relaxed 4-point condition for weighting quartets. Different input orders of taxa lead to trees having distinct topologies which can be evaluated using a maximum likelihood or weighted least squares optimality criterion. Using reduced sets of quartets and a simple heuristic tree search strategy we obtain an overall complexity of O(n 5 log2 n) for the algorithm. We evaluate the performances of the method through comparative tests and show that our method outperforms NJ when a weighted least squares optimality criterion is employed. We also discuss the theoretical boundaries of the algorithm.
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We would like to thank the editor and two anonymous referees for useful comments on earlier versions of this paper.
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Ionescu, T.B., Polaillon, G. & Boulanger, F. Minimum Tree Cost Quartet Puzzling. J Classif 27, 136–157 (2010). https://doi.org/10.1007/s00357-010-9053-9
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DOI: https://doi.org/10.1007/s00357-010-9053-9