• Journal of applied mathematics & informatics
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• 제25권1_2호
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• pp.455-470
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• 2007

In phylogenetic tree construction the neighbor-joining algorithm is the most well known method which constructs a trivalent tree from a pairwise distance data measured by DNA sequences. The core part of the algorithm is its cherry picking criterion based on the tree structure of each quartet. We give a generalized version of the criterion based on the exact box model of quartets, known as the tight span of a metric. We also show by experiment why neighbor-joining and the quartet consistency count method give similar performance.

• 대한수학회논문집
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• 제25권1호
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• pp.149-160
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• 2010

Among the distance based algorithms in phylogenetic tree reconstruction, the neighbor-joining algorithm has been a widely used and effective method. We propose a new algorithm which counts the number of consistent quartets for cherry picking with tie breaking. We show that the success rate of the new algorithm is almost equal to that of neighbor-joining. This gives an explanation of the qualitative nature of neighbor-joining and that of dissimilarity maps from DNA sequence data. Moreover, the new algorithm always reconstructs correct trees from quartet consistent dissimilarity maps.