Communications of the
Korean Mathematical Society CKMS

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.

Keywords: neighbor-joining, phylogenetic tree, quartet consistency count, sequence generation, tree construction algorithm

MSC numbers: 92D15, 68R10, 05C05, 68Q25