A faster construction of greedy consensus trees

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

doi:10.4230/LIPIcs.ICALP.2018.63

A faster construction of greedy consensus trees

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

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-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(kn^1.5) and O(kn) respectively.

Original language	English
Title of host publication	45th International Colloquium on Automata, Languages, and Programming, ICALP 2018
Editors	Christos Kaklamanis, Daniel Marx, Ioannis Chatzigiannakis, Donald Sannella
Publisher	Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
Pages	63:1–63:14
ISBN (Electronic)	9783959770767
DOIs	https://doi.org/10.4230/LIPIcs.ICALP.2018.63
State	Published - 1 Jul 2018
Event	45th International Colloquium on Automata, Languages, and Programming, ICALP 2018 - Prague, Czech Republic Duration: 9 Jul 2018 → 13 Jul 2018

Publication series

Name	Leibniz International Proceedings in Informatics, LIPIcs
Volume	107
ISSN (Print)	1868-8969

Conference

Conference	45th International Colloquium on Automata, Languages, and Programming, ICALP 2018
Country/Territory	Czech Republic
City	Prague
Period	9/07/18 → 13/07/18

Bibliographical note

Funding Information:
Supported in part by Israel Science Foundation grant 592/17

Publisher Copyright:
© Paweł Gawrychowski, Gad M. Landau, Wing-Kin Sung, and Oren Weimann;.

Keywords

Dynamic trees
Greedy consensus trees
Phylogenetic trees

ASJC Scopus subject areas

Software

Access to Document

10.4230/LIPIcs.ICALP.2018.63

Cite this

Gawrychowski, P., Landau, G. M., Sung, W. K., & Weimann, O. (2018). A faster construction of greedy consensus trees. In C. Kaklamanis, D. Marx, I. Chatzigiannakis, & D. Sannella (Eds.), 45th International Colloquium on Automata, Languages, and Programming, ICALP 2018 (pp. 63:1–63:14). (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 107). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.ICALP.2018.63

Gawrychowski, Paweł ; Landau, Gad M. ; Sung, Wing Kin et al. / A faster construction of greedy consensus trees. 45th International Colloquium on Automata, Languages, and Programming, ICALP 2018. editor / Christos Kaklamanis ; Daniel Marx ; Ioannis Chatzigiannakis ; Donald Sannella. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2018. pp. 63:1–63:14 (Leibniz International Proceedings in Informatics, LIPIcs).

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title = "A faster construction of greedy consensus trees",

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.",

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Gawrychowski, P, Landau, GM, Sung, WK & Weimann, O 2018, A faster construction of greedy consensus trees. in C Kaklamanis, D Marx, I Chatzigiannakis & D Sannella (eds), 45th International Colloquium on Automata, Languages, and Programming, ICALP 2018. Leibniz International Proceedings in Informatics, LIPIcs, vol. 107, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, pp. 63:1–63:14, 45th International Colloquium on Automata, Languages, and Programming, ICALP 2018, Prague, Czech Republic, 9/07/18. https://doi.org/10.4230/LIPIcs.ICALP.2018.63

A faster construction of greedy consensus trees. / Gawrychowski, Paweł; Landau, Gad M.; Sung, Wing Kin et al.
45th International Colloquium on Automata, Languages, and Programming, ICALP 2018. ed. / Christos Kaklamanis; Daniel Marx; Ioannis Chatzigiannakis; Donald Sannella. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2018. p. 63:1–63:14 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 107).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - A faster construction of greedy consensus trees

AU - Gawrychowski, Paweł

AU - Landau, Gad M.

AU - Sung, Wing Kin

AU - Weimann, Oren

N1 - Funding Information: Supported in part by Israel Science Foundation grant 592/17 Publisher Copyright: © Paweł Gawrychowski, Gad M. Landau, Wing-Kin Sung, and Oren Weimann;.

PY - 2018/7/1

Y1 - 2018/7/1

N2 - 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.

AB - 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.

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KW - Phylogenetic trees

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M3 - Conference contribution

AN - SCOPUS:85049774980

T3 - Leibniz International Proceedings in Informatics, LIPIcs

SP - 63:1–63:14

BT - 45th International Colloquium on Automata, Languages, and Programming, ICALP 2018

A2 - Kaklamanis, Christos

A2 - Marx, Daniel

A2 - Chatzigiannakis, Ioannis

A2 - Sannella, Donald

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T2 - 45th International Colloquium on Automata, Languages, and Programming, ICALP 2018

Y2 - 9 July 2018 through 13 July 2018

ER -

Gawrychowski P, Landau GM, Sung WK, Weimann O. A faster construction of greedy consensus trees. In Kaklamanis C, Marx D, Chatzigiannakis I, Sannella D, editors, 45th International Colloquium on Automata, Languages, and Programming, ICALP 2018. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. 2018. p. 63:1–63:14. (Leibniz International Proceedings in Informatics, LIPIcs). doi: 10.4230/LIPIcs.ICALP.2018.63

A faster construction of greedy consensus trees

Abstract

Publication series

Conference

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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