Extracting conflict-free information from multi-labeled trees

Akshay Deepak, David Fernández-Baca, Michelle M. McMahon

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

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. 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.

Original languageEnglish (US)
Title of host publicationAlgorithms in Bioinformatics - 12th International Workshop, WABI 2012, Proceedings
Pages81-92
Number of pages12
DOIs
StatePublished - Oct 1 2012
Event12th International Workshop on Algorithms in Bioinformatics, WABI 2012 - Ljubljana, Slovenia
Duration: Sep 10 2012Sep 12 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7534 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other12th International Workshop on Algorithms in Bioinformatics, WABI 2012
CountrySlovenia
CityLjubljana
Period9/10/129/12/12

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Deepak, A., Fernández-Baca, D., & McMahon, M. M. (2012). Extracting conflict-free information from multi-labeled trees. In Algorithms in Bioinformatics - 12th International Workshop, WABI 2012, Proceedings (pp. 81-92). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7534 LNBI). https://doi.org/10.1007/978-3-642-33122-0_7