A faster construction of greedy consensus trees

Paweł Gawrychowski, Gad M. Landau, Wing Kin Sung, Oren Weimann

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It is also central for predicting a species tree from a set of gene trees, as indicated recently in [Nature 2013]. This paper focuses on two of the most well-known and widely used consensus tree methods: the greedy consensus tree and the frequency di erence consensus tree. Given k conflicting trees each with n leaves, the previous fastest algorithms for these problems were O(kn2) for the greedy consensus tree [J. ACM 2016] and O(min(kn2, k2n)) for the frequency di erence consensus tree [ACM TCBB 2016]. We improve these running times to O(kn1.5) and O(kn) respectively.

Original languageAmerican English
Title of host publication45th International Colloquium on Automata, Languages, and Programming, ICALP 2018
EditorsChristos Kaklamanis, Daniel Marx, Ioannis Chatzigiannakis, Donald Sannella
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
Pages63:1–63:14
ISBN (Electronic)9783959770767
DOIs
StatePublished - 1 Jul 2018
Event45th International Colloquium on Automata, Languages, and Programming, ICALP 2018 - Prague, Czech Republic
Duration: 9 Jul 201813 Jul 2018

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume107

Conference

Conference45th International Colloquium on Automata, Languages, and Programming, ICALP 2018
Country/TerritoryCzech Republic
CityPrague
Period9/07/1813/07/18

Keywords

  • Dynamic trees
  • Greedy consensus trees
  • Phylogenetic trees

All Science Journal Classification (ASJC) codes

  • Software

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