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Near-Optimal Algorithm for Constructing Greedy Consensus Tree

Author Hongxun Wu

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Hongxun Wu
  • Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China

Acknowledgements

We want to thank anonymous reviewers for many helpful comments.

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Hongxun Wu. Near-Optimal Algorithm for Constructing Greedy Consensus Tree. In 47th International Colloquium on Automata, Languages, and Programming (ICALP 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 168, pp. 105:1-105:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020) https://doi.org/10.4230/LIPIcs.ICALP.2020.105

Abstract

In biology, phylogenetic trees are important tools for describing evolutionary relations, but various data sources may result in conflicting phylogenetic trees. To summarize these conflicting phylogenetic trees, consensus tree methods take k conflicting phylogenetic trees (each with n leaves) as input and output a single phylogenetic tree as consensus. 
Among the consensus tree methods, a widely used method is the greedy consensus tree. The previous fastest algorithms for constructing a greedy consensus tree have time complexity Õ(kn^1.5) [Gawrychowski, Landau, Sung, Weimann 2018] and Õ(k²n) [Sung 2019] respectively. In this paper, we improve the running time to Õ(kn). Since k input trees have Θ(kn) nodes in total, our algorithm is optimal up to polylogarithmic factors.

Subject Classification

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

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