A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees
Background Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve inst...
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| Veröffentlicht in: | BMC bioinformatics Jg. 15; H. 1; S. 127 |
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| Sprache: | Englisch |
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BioMed Central
05.05.2014
BioMed Central Ltd Springer Nature B.V |
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| Abstract | Background
Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50.
Results
Here we present
CycleKiller
and
NonbinaryCycleKiller
, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations.
Conclusions
Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present
TerminusEst
, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the
NonbinaryCycleKiller
algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data. |
|---|---|
| AbstractList | Background: Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Results: Here we present CYCLEKILLER and NONBINARYCYCLEKILLER, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Conclusions: Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TERMINUSEST, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NONBINARYCYCLEKILLER algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data. Doc number: 127 Abstract Background: Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Results: Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Conclusions: Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data. Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data. Background Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Results Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Conclusions Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data. Keywords: Hybridization number, Phylogenetic networks, Approximation algorithms, Directed feedback vertex set Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data. Background Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Results Here we present CycleKiller and NonbinaryCycleKiller , the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Conclusions Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst , which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data. Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50.BACKGROUNDReticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50.Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations.RESULTSHere we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations.Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data.CONCLUSIONSUsing simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data. |
| ArticleNumber | 127 |
| Audience | Academic |
| Author | Lekić, Nela Kelk, Steven Scornavacca, Celine Iersel, Leo van |
| AuthorAffiliation | 3 ISEM, CNRS – Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier, France 1 Centrum Wiskunde & Informatica (CWI), P.O. Box 94079, 1090 GB, Amsterdam, The Netherlands 2 Department of Knowledge Engineering (DKE), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands |
| AuthorAffiliation_xml | – name: 1 Centrum Wiskunde & Informatica (CWI), P.O. Box 94079, 1090 GB, Amsterdam, The Netherlands – name: 2 Department of Knowledge Engineering (DKE), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands – name: 3 ISEM, CNRS – Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier, France |
| Author_xml | – sequence: 1 givenname: Leo van surname: Iersel fullname: Iersel, Leo van email: l.j.j.v.iersel@gmail.com organization: Centrum Wiskunde & Informatica (CWI) – sequence: 2 givenname: Steven surname: Kelk fullname: Kelk, Steven organization: Department of Knowledge Engineering (DKE), Maastricht University – sequence: 3 givenname: Nela surname: Lekić fullname: Lekić, Nela organization: Department of Knowledge Engineering (DKE), Maastricht University – sequence: 4 givenname: Celine surname: Scornavacca fullname: Scornavacca, Celine organization: ISEM, CNRS – Université Montpellier II, Place Eugène Bataillon |
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| Cites_doi | 10.1177/117693430700300017 10.1109/TCBB.2012.134 10.1089/cmb.2012.0240 10.1007/978-3-642-13193-6_13 10.1137/120903567 10.1016/j.ic.2010.11.022 10.1093/bioinformatics/btr618 10.1137/120864350 10.1093/gbe/evq077 10.1137/110845045 10.1016/j.dam.2006.08.008 10.1093/bioinformatics/btq548 10.1007/PL00009191 10.1007/s00285-005-0315-9 10.1109/TCBB.2008.86 10.1007/978-1-4612-0515-9 10.1093/sysbio/sys062 10.1016/j.tig.2013.05.007 10.1109/TCBB.2011.137 10.1089/cmb.2009.0166 |
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| Copyright | van Iersel et al.; licensee BioMed Central Ltd. 2014 COPYRIGHT 2014 BioMed Central Ltd. 2014 van Iersel et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Distributed under a Creative Commons Attribution 4.0 International License Copyright © 2014 van Iersel et al.; licensee BioMed Central Ltd. 2014 van Iersel et al.; licensee BioMed Central Ltd. |
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| Keywords | Phylogenetic networks Hybridization number Approximation algorithms Directed feedback vertex set |
| Language | English |
| License | Distributed under a Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
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Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to... Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain... Background Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to... Doc number: 127 Abstract Background: Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum... Background: Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to... |
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| SubjectTerms | Algorithms Analysis Bioinformatics Biologists Biology Biomedical and Life Sciences Comparative genomics Computational Biology/Bioinformatics Computer Appl. in Life Sciences Computer Science Evolution Genetic aspects Hybridization Hybridization, Genetic Life Sciences Methods Microarrays Phylogenetics Phylogeny Research Article Software |
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| Title | A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees |
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