Improved algorithms for constructing consensus trees

Jesper Andreas Jansson, Chuanqi Shen, Wing Kin Sung

Research output: Journal article publicationJournal articleAcademic researchpeer-review

12 Citations (Scopus)

Abstract

A consensus tree is a single phylogenetic tree that summarizes the branching structure in a given set of conflicting phylogenetic trees. Many different types of consensus trees have been proposed in the literature; three of the most well-known and widely used ones are the majority rule consensus tree, the loose consensus tree, and the greedy consensus tree. This article presents new deterministic algorithms for constructing them that are faster than all the previously known ones. Given κ phylogenetic trees with n leaves each and with identical leaf label sets, our algorithms run in O(nκ) time (majority rule consensus tree), O(nκ) time (loose consensus tree), and O(n2κ) time (greedy consensus tree). Our algorithms for the majority rule consensus and the loose consensus trees are optimal since the input size is Ω(nκ). Experimental results show that the algorithms are fast in practice.
Original languageEnglish
Article number28
JournalJournal of the ACM
Volume63
Issue number3
DOIs
Publication statusPublished - 1 Jun 2016
Externally publishedYes

Keywords

  • Cluster
  • Greedy consensus tree
  • Implementation
  • Loose consensus tree
  • Majority rule consensus tree
  • Pairwise compatibility
  • Phylogenetic tree

ASJC Scopus subject areas

  • Control and Systems Engineering
  • Software
  • Information Systems
  • Hardware and Architecture
  • Artificial Intelligence

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