The complexity of inferring a minimally resolved phylogenetic supertree

Jesper Andreas Jansson, Richard S. Lemence, Andrzej Lingas

Research output: Journal article publicationJournal articleAcademic researchpeer-review

12 Citations (Scopus)

Abstract

A recursive algorithm by Aho et al. [SIAM J. Comput., 10 (1981), pp. 405-421] forms the basis for many modern rooted supertree methods employed in Phylogenetics. However, as observed by Bryant [Building Trees, Hunting for Trees, and Comparing Trees: Theory and Methods in Phylogenetic Analysis, Ph.D. thesis, University of Canterbury, Christchurch, New Zealand, 1997], the tree output by the algorithm of Aho et al. is not always minimal; there may exist other trees which contain fewer nodes yet are still consistent with the input. In this paper, we prove strong polynomialtime inapproximability results for the problem of inferring a minimally resolved supertree from a given consistent set of rooted triplets (MinRS). Furthermore, we show that the decision version of MinRS is NP-hard for any fixed positive integer q = 4, where q is the number of allowed internal nodes, but linear-time solvable for q = 3. In contrast, MinRS becomes polynomial-time solvable for any q when restricted to caterpillars. We also present an exponential-time algorithm based on tree separators for solving MinRS exactly. It runs in 2O(n log p) time when every node may have at most p children that are internal nodes and where n is the cardinality of the leaf label set. Finally, we demonstrate that augmenting the algorithm of Aho et al. with an algorithm for optimal graph coloring to help merge certain blocks of leaves during the execution does not improve the output solution much in the worst case.
Original languageEnglish
Pages (from-to)272-291
Number of pages20
JournalSIAM Journal on Computing
Volume41
Issue number1
DOIs
Publication statusPublished - 4 Jun 2012
Externally publishedYes

Keywords

  • Graph coloring
  • Minimally resolved supertree
  • NP-hardness
  • Phylogenetic tree
  • Rooted triplet
  • Tree separator

ASJC Scopus subject areas

  • Computer Science(all)
  • Mathematics(all)

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