Building a small and informative phylogenetic supertree

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Building a small and informative phylogenetic supertree. / Jansson, Jesper; Mampentzidis, Konstantinos; Sandhya, T. P.

19th International Workshop on Algorithms in Bioinformatics, WABI 2019. red. / Katharina T. Huber; Dan Gusfield. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2019. 1 (Leibniz International Proceedings in Informatics, LIPIcs, Bind 143).

Publikation: Bidrag til bog/antologi/rapport/proceedingKonferencebidrag i proceedingsForskningpeer review

Harvard

Jansson, J, Mampentzidis, K & Sandhya, TP 2019, Building a small and informative phylogenetic supertree. i KT Huber & D Gusfield (red), 19th International Workshop on Algorithms in Bioinformatics, WABI 2019., 1, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, Leibniz International Proceedings in Informatics, LIPIcs, bind 143, 19th International Workshop on Algorithms in Bioinformatics, WABI 2019, Niagara Falls, USA, 08/09/2019. https://doi.org/10.4230/LIPIcs.WABI.2019.1

APA

Jansson, J., Mampentzidis, K., & Sandhya, T. P. (2019). Building a small and informative phylogenetic supertree. I K. T. Huber, & D. Gusfield (red.), 19th International Workshop on Algorithms in Bioinformatics, WABI 2019 [1] Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. Leibniz International Proceedings in Informatics, LIPIcs, Bind. 143 https://doi.org/10.4230/LIPIcs.WABI.2019.1

CBE

Jansson J, Mampentzidis K, Sandhya TP. 2019. Building a small and informative phylogenetic supertree. Huber KT, Gusfield D, red. I 19th International Workshop on Algorithms in Bioinformatics, WABI 2019. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. Article 1. (Leibniz International Proceedings in Informatics, LIPIcs, Bind 143). https://doi.org/10.4230/LIPIcs.WABI.2019.1

MLA

Jansson, Jesper, Konstantinos Mampentzidis og T. P. Sandhya "Building a small and informative phylogenetic supertree". og Huber, Katharina T. Gusfield, Dan (red.). 19th International Workshop on Algorithms in Bioinformatics, WABI 2019. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. (Leibniz International Proceedings in Informatics, LIPIcs, Bind 143). 2019. https://doi.org/10.4230/LIPIcs.WABI.2019.1

Vancouver

Jansson J, Mampentzidis K, Sandhya TP. Building a small and informative phylogenetic supertree. I Huber KT, Gusfield D, red., 19th International Workshop on Algorithms in Bioinformatics, WABI 2019. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. 2019. 1. (Leibniz International Proceedings in Informatics, LIPIcs, Bind 143). https://doi.org/10.4230/LIPIcs.WABI.2019.1

Author

Jansson, Jesper ; Mampentzidis, Konstantinos ; Sandhya, T. P. / Building a small and informative phylogenetic supertree. 19th International Workshop on Algorithms in Bioinformatics, WABI 2019. red. / Katharina T. Huber ; Dan Gusfield. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2019. (Leibniz International Proceedings in Informatics, LIPIcs, Bind 143).

Bibtex

@inproceedings{4698851d198641fa82d6f456d42664cf,
title = "Building a small and informative phylogenetic supertree",
abstract = "We combine two fundamental, previously studied optimization problems related to the construction of phylogenetic trees called maximum rooted triplets consistency (MAXRTC) and minimally resolved supertree (MINRS) into a new problem, which we call q-maximum rooted triplets consistency (q-MAXRTC). The input to our new problem is a set R of resolved triplets (rooted, binary phylogenetic trees with three leaves each) and the objective is to find a phylogenetic tree with exactly q internal nodes that contains the largest possible number of triplets from R. We first prove that q-MAXRTC is NP-hard even to approximate within a constant ratio for every fixed q ≥ 2, and then develop various polynomial-time approximation algorithms for different values of q. Next, we show experimentally that representing a phylogenetic tree by one having much fewer nodes typically does not destroy too much triplet branching information. As an extreme example, we show that allowing only nine internal nodes is still sufficient to capture on average 80% of the rooted triplets from some recently published trees, each having between 760 and 3081 internal nodes. Finally, to demonstrate the algorithmic advantage of using trees with few internal nodes, we propose a new algorithm for computing the rooted triplet distance between two phylogenetic trees over a leaf label set of size n that runs in O(qn) time, where q is the number of internal nodes in the smaller tree, and is therefore faster than the currently best algorithms for the problem (with O(n log n) time complexity [SODA 2013, ESA 2017]) whenever q = o(log n).",
keywords = "Approximation algorithm, Phylogenetic tree, Rooted triplet, Supertree",
author = "Jesper Jansson and Konstantinos Mampentzidis and Sandhya, {T. P.}",
year = "2019",
month = sep,
doi = "10.4230/LIPIcs.WABI.2019.1",
language = "English",
series = "Leibniz International Proceedings in Informatics, LIPIcs",
publisher = "Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing",
editor = "Huber, {Katharina T.} and Dan Gusfield",
booktitle = "19th International Workshop on Algorithms in Bioinformatics, WABI 2019",
note = "19th International Workshop on Algorithms in Bioinformatics, WABI 2019 ; Conference date: 08-09-2019 Through 10-09-2019",

}

RIS

TY - GEN

T1 - Building a small and informative phylogenetic supertree

AU - Jansson, Jesper

AU - Mampentzidis, Konstantinos

AU - Sandhya, T. P.

PY - 2019/9

Y1 - 2019/9

N2 - We combine two fundamental, previously studied optimization problems related to the construction of phylogenetic trees called maximum rooted triplets consistency (MAXRTC) and minimally resolved supertree (MINRS) into a new problem, which we call q-maximum rooted triplets consistency (q-MAXRTC). The input to our new problem is a set R of resolved triplets (rooted, binary phylogenetic trees with three leaves each) and the objective is to find a phylogenetic tree with exactly q internal nodes that contains the largest possible number of triplets from R. We first prove that q-MAXRTC is NP-hard even to approximate within a constant ratio for every fixed q ≥ 2, and then develop various polynomial-time approximation algorithms for different values of q. Next, we show experimentally that representing a phylogenetic tree by one having much fewer nodes typically does not destroy too much triplet branching information. As an extreme example, we show that allowing only nine internal nodes is still sufficient to capture on average 80% of the rooted triplets from some recently published trees, each having between 760 and 3081 internal nodes. Finally, to demonstrate the algorithmic advantage of using trees with few internal nodes, we propose a new algorithm for computing the rooted triplet distance between two phylogenetic trees over a leaf label set of size n that runs in O(qn) time, where q is the number of internal nodes in the smaller tree, and is therefore faster than the currently best algorithms for the problem (with O(n log n) time complexity [SODA 2013, ESA 2017]) whenever q = o(log n).

AB - We combine two fundamental, previously studied optimization problems related to the construction of phylogenetic trees called maximum rooted triplets consistency (MAXRTC) and minimally resolved supertree (MINRS) into a new problem, which we call q-maximum rooted triplets consistency (q-MAXRTC). The input to our new problem is a set R of resolved triplets (rooted, binary phylogenetic trees with three leaves each) and the objective is to find a phylogenetic tree with exactly q internal nodes that contains the largest possible number of triplets from R. We first prove that q-MAXRTC is NP-hard even to approximate within a constant ratio for every fixed q ≥ 2, and then develop various polynomial-time approximation algorithms for different values of q. Next, we show experimentally that representing a phylogenetic tree by one having much fewer nodes typically does not destroy too much triplet branching information. As an extreme example, we show that allowing only nine internal nodes is still sufficient to capture on average 80% of the rooted triplets from some recently published trees, each having between 760 and 3081 internal nodes. Finally, to demonstrate the algorithmic advantage of using trees with few internal nodes, we propose a new algorithm for computing the rooted triplet distance between two phylogenetic trees over a leaf label set of size n that runs in O(qn) time, where q is the number of internal nodes in the smaller tree, and is therefore faster than the currently best algorithms for the problem (with O(n log n) time complexity [SODA 2013, ESA 2017]) whenever q = o(log n).

KW - Approximation algorithm

KW - Phylogenetic tree

KW - Rooted triplet

KW - Supertree

UR - http://www.scopus.com/inward/record.url?scp=85072630503&partnerID=8YFLogxK

U2 - 10.4230/LIPIcs.WABI.2019.1

DO - 10.4230/LIPIcs.WABI.2019.1

M3 - Article in proceedings

AN - SCOPUS:85072630503

T3 - Leibniz International Proceedings in Informatics, LIPIcs

BT - 19th International Workshop on Algorithms in Bioinformatics, WABI 2019

A2 - Huber, Katharina T.

A2 - Gusfield, Dan

PB - Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing

T2 - 19th International Workshop on Algorithms in Bioinformatics, WABI 2019

Y2 - 8 September 2019 through 10 September 2019

ER -