SAQ: semi-algebraic quartet reconstruction

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Autores: Casanellas Rius, Marta|||0000-0002-1724-8358, Fernández Sánchez, Jesús|||0000-0002-7062-8042, Garrote López, Marina
Tipo de recurso: artículo
Fecha de publicación:2021
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/361166
Acceso en línea:https://hdl.handle.net/2117/361166
https://dx.doi.org/10.1109/TCBB.2021.3101278
Access Level:acceso abierto
Palabra clave:Algebraic topology
Topology
Markov processes
Reconstruction algorithms
Phylogeny
Symmetric matrices
Data models
Genetics
Topologia algèbrica
Topologia
Classificació AMS::55 Algebraic topology::55S Operations and obstructions
Classificació AMS::54 General topology::54H Connections with other structures, applications
Àrees temàtiques de la UPC::Matemàtiques i estadística::Geometria::Geometria algebraica
Àrees temàtiques de la UPC::Matemàtiques i estadística::Topologia::Topologia algebraica
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spelling SAQ: semi-algebraic quartet reconstructionCasanellas Rius, Marta|||0000-0002-1724-8358Fernández Sánchez, Jesús|||0000-0002-7062-8042Garrote López, MarinaAlgebraic topologyTopologyMarkov processesReconstruction algorithmsPhylogenySymmetric matricesData modelsGeneticsTopologia algèbricaTopologiaClassificació AMS::55 Algebraic topology::55S Operations and obstructionsClassificació AMS::54 General topology::54H Connections with other structures, applicationsÀrees temàtiques de la UPC::Matemàtiques i estadística::Geometria::Geometria algebraicaÀrees temàtiques de la UPC::Matemàtiques i estadística::Topologia::Topologia algebraica© 2021 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.We present the phylogenetic quartet reconstruction method SAQ (Semi-Algebraic Quartet reconstruction). SAQ is consistent with the most general Markov model of nucleotide substitution and, in particular, it allows for rate heterogeneity across lineages. Based on the algebraic and semi-algebraic description of distributions that arise from the general Markov model on a quartet, the method outputs normalized weights for the three trivalent quartets (which can be used as input of quartet-based methods). We show that SAQ is a highly competitive method that outperforms most of the well known reconstruction methods on data simulated under the general Markov model on 4-taxon trees. Moreover, it also achieves a high performance on data that violates the underlying assumptions.The authors were partially supported by Spanish government Secretar´ıa de Estado de Investigaci´on, Desarrollo e Innovaci´on [MTM2015-69135-P (MINECO/FEDER)] and [PID2019- 103849GB-I00 (MINECO)]; Generalitat de Catalunya [2014 SGR-634]. M. Garrote-L´opez was also funded by Spanish government, Ministerio de Econom´ıa y Competitividad research project Maria de Maeztu [MDM-2014-0445].Peer Reviewed20212021-01-0120222022-02-01journal articlehttp://purl.org/coar/resource_type/c_6501AMhttp://purl.org/coar/version/c_ab4af688f83e57aainfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/361166https://dx.doi.org/10.1109/TCBB.2021.3101278reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)InglésengMinisterio de Economía y Competitividad http://doi.org/10.13039/501100003329 MTM2015-69135-P GEOMETRIA Y TOPOLOGIA DE VARIEDADES, ALGEBRA Y APLICACIONESopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivs 4.0 Internationalhttps://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/3611662026-05-27T15:37:01Z
dc.title.none.fl_str_mv SAQ: semi-algebraic quartet reconstruction
title SAQ: semi-algebraic quartet reconstruction
spellingShingle SAQ: semi-algebraic quartet reconstruction
Casanellas Rius, Marta|||0000-0002-1724-8358
Algebraic topology
Topology
Markov processes
Reconstruction algorithms
Phylogeny
Symmetric matrices
Data models
Genetics
Topologia algèbrica
Topologia
Classificació AMS::55 Algebraic topology::55S Operations and obstructions
Classificació AMS::54 General topology::54H Connections with other structures, applications
Àrees temàtiques de la UPC::Matemàtiques i estadística::Geometria::Geometria algebraica
Àrees temàtiques de la UPC::Matemàtiques i estadística::Topologia::Topologia algebraica
title_short SAQ: semi-algebraic quartet reconstruction
title_full SAQ: semi-algebraic quartet reconstruction
title_fullStr SAQ: semi-algebraic quartet reconstruction
title_full_unstemmed SAQ: semi-algebraic quartet reconstruction
title_sort SAQ: semi-algebraic quartet reconstruction
dc.creator.none.fl_str_mv Casanellas Rius, Marta|||0000-0002-1724-8358
Fernández Sánchez, Jesús|||0000-0002-7062-8042
Garrote López, Marina
author Casanellas Rius, Marta|||0000-0002-1724-8358
author_facet Casanellas Rius, Marta|||0000-0002-1724-8358
Fernández Sánchez, Jesús|||0000-0002-7062-8042
Garrote López, Marina
author_role author
author2 Fernández Sánchez, Jesús|||0000-0002-7062-8042
Garrote López, Marina
author2_role author
author
dc.subject.none.fl_str_mv Algebraic topology
Topology
Markov processes
Reconstruction algorithms
Phylogeny
Symmetric matrices
Data models
Genetics
Topologia algèbrica
Topologia
Classificació AMS::55 Algebraic topology::55S Operations and obstructions
Classificació AMS::54 General topology::54H Connections with other structures, applications
Àrees temàtiques de la UPC::Matemàtiques i estadística::Geometria::Geometria algebraica
Àrees temàtiques de la UPC::Matemàtiques i estadística::Topologia::Topologia algebraica
topic Algebraic topology
Topology
Markov processes
Reconstruction algorithms
Phylogeny
Symmetric matrices
Data models
Genetics
Topologia algèbrica
Topologia
Classificació AMS::55 Algebraic topology::55S Operations and obstructions
Classificació AMS::54 General topology::54H Connections with other structures, applications
Àrees temàtiques de la UPC::Matemàtiques i estadística::Geometria::Geometria algebraica
Àrees temàtiques de la UPC::Matemàtiques i estadística::Topologia::Topologia algebraica
description © 2021 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
publishDate 2021
dc.date.none.fl_str_mv 2021
2021-01-01
2022
2022-02-01
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
AM
http://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/361166
https://dx.doi.org/10.1109/TCBB.2021.3101278
url https://hdl.handle.net/2117/361166
https://dx.doi.org/10.1109/TCBB.2021.3101278
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Ministerio de Economía y Competitividad http://doi.org/10.13039/501100003329 MTM2015-69135-P GEOMETRIA Y TOPOLOGIA DE VARIEDADES, ALGEBRA Y APLICACIONES
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 4.0 International
https://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 4.0 International
https://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
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