Correcting gene tree by removal and modification: Tractability and approximability

Stefano Beretta, Mauro Castelli, Riccardo Dondi

Research output: Contribution to journalArticle

Abstract

Gene tree correction with respect to a given species tree is a problem that has been recently proposed in order to better understand the evolution of gene families. One of the combinatorial methods proposed to tackle with this problem aims to correct a gene tree by removing the minimum number of leaves/labels (Minimum Leaf Removal and Minimum Label Removal, respectively). The two problems have been shown to be APX-hard, and fixed-parameter tractable, when parameterized by the number of leaves/labels removed. In this paper, we focus on the approximation complexity of these two problems and we show that they are not approximable within factor blog m, where m is the number of leaves of the species tree and b>0 is a constant. Furthermore, we introduce and study two new variants of the problem, where the goal is the correction of a gene tree with the minimum number of leaf/label modifications (Minimum Leaf Modification and Minimum Label Modification, respectively). We show that the two modification problems, differently from the removal versions, are unlikely to be fixed-parameter tractable. More precisely, we prove that the Minimum Leaf Modification problem is W[1]-hard, when parameterized by the number of leaf modifications, and that the Minimum Label Modification problem is W[2]-hard, when parameterized by the number of label modifications.

Original languageEnglish
Pages (from-to)115-129
Number of pages15
JournalJournal Of Discrete Algorithms
Volume33
DOIs
Publication statusPublished - 1 Jul 2015

Keywords

  • Approximation complexity
  • Computational biology
  • Gene tree correction
  • Gene tree reconciliation
  • Parameterized complexity

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