Affiliation
Department of Computer Science, Iowa State University, Ames, Iowa, USASchool of Plant Sciences, University of Arizona, Tucson, Arizona, USA
Issue Date
2013
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BioMed CentralCitation
Deepak et al. Algorithms for Molecular Biology 2013, 8:18 http://www.almob.org/content/8/18Journal
Algorithms for Molecular BiologyRights
© 2013 Deepak et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0).Collection Information
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.Abstract
BACKGROUND:A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set of taxa, but can also contain conflict-free information that is of interest and yet is not obvious.RESULTS:We define the information content of a MUL-tree T as the set of all conflict-free quartet topologies implied by T, and define the maximal reduced form of T as the smallest tree that can be obtained from T by pruning leaves and contracting edges while retaining the same information content. We show that any two MUL-trees with the same information content exhibit the same reduced form. This introduces an equivalence relation among MUL-trees with potential applications to comparing MUL-trees. We present an efficient algorithm to reduce a MUL-tree to its maximally reduced form and evaluate its performance on empirical datasets in terms of both quality of the reduced tree and the degree of data reduction achieved.CONCLUSIONS:Our measure of conflict-free information content based on quartets is simple and topologically appealing. In the experiments, the maximally reduced form is often much smaller than the original tree, yet retains most of the taxa. The reduction algorithm is quadratic in the number of leaves and its complexity is unaffected by the multiplicity of leaf labels or the degree of the nodes.EISSN
1748-7188Version
Final published versionAdditional Links
http://www.almob.org/content/8/1/18ae974a485f413a2113503eed53cd6c53
10.1186/1748-7188-8-18
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Except where otherwise noted, this item's license is described as © 2013 Deepak et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0).