Computing the Quartet Distance Between Trees of Arbitrary Degree
- 773 Downloads
We present two algorithms for computing the quartet distance between trees of arbitrary degree. The quartet distance between two unrooted evolutionary trees is the number of quartets—sub-trees induced by four leaves—that differs between the trees. Previous algorithms focus on computing the quartet distance between binary trees. In this paper, we present two algorithms for computing the quartet distance between trees of arbitrary degrees. One in time O(n 3) and space O(n 2) and one in time O(n 2 d 2) and space O(n 2), where n is the number of species and d is the maximal degree of the internal nodes of the trees. We experimentally compare the two algorithms and discuss possible directions for improving the running time further.
KeywordsBinary Tree Internal Node Directed Edge Extended Tree Original Tree
Unable to display preview. Download preview PDF.
- 2.Berry, V., Bryant, D.: Faster reliable phylogenetic analysis. In: Proc. 3rd International Conference on Computational Molecular Biology, RECOMB (1999)Google Scholar
- 5.Bryant, D., Tsang, J., Kearney, P.E., Li, M.: Computing the quartet distance between evolutionary trees. In: Proceedings of the 11th Annual Symposium on Discrete Algorithms (SODA), pp. 285–286 (2000)Google Scholar
- 6.Buneman, P.: The recovery of trees from measures of dissimilarity. In: Hodson, F., Kendall, D., Tautu, P. (eds.) Mathematics in Archaeological and Historical Sciences, pp. 387–395. Edinburgh University Press, Edinburgh (1971)Google Scholar
- 8.Felsenstein, J.: Inferring Phylogenies. Sinauer Associates Inc. (2004)Google Scholar