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A Faster Construction of Greedy Consensus Trees

Authors Pawel Gawrychowski, Gad M. Landau, Wing-Kin Sung, Oren Weimann

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ACM Subject Classification
  • Theory of computation → Design and analysis of algorithms
Keywords
  • phylogenetic trees
  • greedy consensus trees
  • dynamic trees

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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 difference consensus tree. Given k conflicting trees each with n leaves, the previous fastest algorithms for these problems were O(k n^2) for the greedy consensus tree [J. ACM 2016] and O~(min{k n^2, k^2n}) for the frequency difference consensus tree [ACM TCBB 2016]. We improve these running times to O~(k n^{1.5}) and O~(k n) respectively.

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Pawel Gawrychowski, Gad M. Landau, Wing-Kin Sung, and Oren Weimann. A Faster Construction of Greedy Consensus Trees. In 45th International Colloquium on Automata, Languages, and Programming (ICALP 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 107, pp. 63:1-63:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018) https://doi.org/10.4230/LIPIcs.ICALP.2018.63

Author Details

Pawel Gawrychowski
  • Institute of Computer Science, University of Wrocław, Poland
Gad M. Landau
  • University of Haifa, Israel
Wing-Kin Sung
  • National University of Singapore, Singapore
Oren Weimann
  • University of Haifa, Israel

Funding

  • Weimann, Oren: Supported in part by Israel Science Foundation grant 592/17

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