Conference Paper

Computing the Quartet Distance Between Evolutionary Trees of Bounded Degree.

DOI: 10.1142/9781860947995_0013 Conference: Proceedings of 5th Asia-Pacific Bioinformatics Conference, APBC 2007, 15-17 January 2007, Hong Kong, China
Source: DBLP
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    ABSTRACT: A phylogenetic tree represents historical evolutionary relationship between different species or organisms. There are various methods for reconstructing phylogenetic trees. Applying those techniques usually results in different trees for the same input data. An important problem is to determine how distant two trees reconstructed in such a way are from each other. Comparing phylogenetic trees is also useful in mining phylogenetic information databases. In this paper new metrics for comparing phylogenetic trees are suggested. These metrics are based on a minimum weight perfect matching in bipartite graphs and can be computed in a polynomial time. We study some properties of these metrics and compare them with methods previously known.
    Information Technology, 2008. IT 2008. 1st International Conference on; 06/2008
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    ABSTRACT: Distance measures between trees are useful for comparing trees in a systematic manner, and several different distance measures have been proposed. The triplet and quartet distances, for rooted and unrooted trees, respectively, are defined as the number of subsets of three or four leaves, respectively, where the topologies of the induced subtrees differ. These distances can trivially be computed by explicitly enumerating all sets of three or four leaves and testing if the topologies are different, but this leads to time complexities at least of the order n3 or n4 just for enumerating the sets. The different topologies can be counte dimplicitly, however, and in this paper, we review a series of algorithmic improvements that have been used during the last decade to develop more efficient algorithms by exploiting two different strategies for this; one based on dynamic programming and another based oncoloring leaves in one tree and updating a hierarchical decomposition of the other.
    Biology 12/2013; 2(4):1189-209. DOI:10.3390/biology2041189


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