Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok

Autores
Goloboff, Pablo Augusto; Szumik, Claudia Adriana
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
This paper describes an efficient implementation of triplet-based measures of stability, in the program TNT. The only available implementations of such measures are much slower than the present one, either because of an inefficient implementation (Phyutility, Thor) or because the stability is evaluated with quartets (RogueNaRok, requiring O(t4), instead of the O(t3) possible for triplets). The method to quickly calculate triplets is applied to solving IterPCR (Pol and Escapa, 2009). It is shown that, in some cases, IterPCR or other algorithms in the program TNT (e.g. commands prunnelsen, prunmajor, or chkmoves) produce more informative results than analysis with RogueNaRok.
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científico y Técnicas. Centro Científico Tecnológico Tucumán. Unidad Ejecutora Lillo; Argentina
Fil: Szumik, Claudia Adriana. Consejo Nacional de Investigaciones Científico y Técnicas. Centro Científico Tecnológico Tucumán. Unidad Ejecutora Lillo; Argentina
Materia
Reduced Consensus
Rogue Taxa
Unstable Taxa
Ambiguity
Phylogenetic Analysis
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/12474
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/12474
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRokGoloboff, Pablo AugustoSzumik, Claudia AdrianaReduced ConsensusRogue TaxaUnstable TaxaAmbiguityPhylogenetic Analysishttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1This paper describes an efficient implementation of triplet-based measures of stability, in the program TNT. The only available implementations of such measures are much slower than the present one, either because of an inefficient implementation (Phyutility, Thor) or because the stability is evaluated with quartets (RogueNaRok, requiring O(t4), instead of the O(t3) possible for triplets). The method to quickly calculate triplets is applied to solving IterPCR (Pol and Escapa, 2009). It is shown that, in some cases, IterPCR or other algorithms in the program TNT (e.g. commands prunnelsen, prunmajor, or chkmoves) produce more informative results than analysis with RogueNaRok.Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científico y Técnicas. Centro Científico Tecnológico Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Szumik, Claudia Adriana. Consejo Nacional de Investigaciones Científico y Técnicas. Centro Científico Tecnológico Tucumán. Unidad Ejecutora Lillo; ArgentinaElsevier Inc2015-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/12474Goloboff, Pablo Augusto; Szumik, Claudia Adriana; Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok; Elsevier Inc; Molecular Phylogenetics And Evolution; 88; 7-2015; 93-1041055-7903enginfo:eu-repo/semantics/altIdentifier/doi/10.1016/j.ympev.2015.04.003info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1055790315000998info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-12-23T14:13:19Zoai:ri.conicet.gov.ar:11336/12474instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-12-23 14:13:19.908CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
title Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
spellingShingle Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
Goloboff, Pablo Augusto
Reduced Consensus
Rogue Taxa
Unstable Taxa
Ambiguity
Phylogenetic Analysis
title_short Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
title_full Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
title_fullStr Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
title_full_unstemmed Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
title_sort Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok
dc.creator.none.fl_str_mv Goloboff, Pablo Augusto
Szumik, Claudia Adriana
author Goloboff, Pablo Augusto
author_facet Goloboff, Pablo Augusto
Szumik, Claudia Adriana
author_role author
author2 Szumik, Claudia Adriana
author2_role author
dc.subject.none.fl_str_mv Reduced Consensus
Rogue Taxa
Unstable Taxa
Ambiguity
Phylogenetic Analysis
topic Reduced Consensus
Rogue Taxa
Unstable Taxa
Ambiguity
Phylogenetic Analysis
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv This paper describes an efficient implementation of triplet-based measures of stability, in the program TNT. The only available implementations of such measures are much slower than the present one, either because of an inefficient implementation (Phyutility, Thor) or because the stability is evaluated with quartets (RogueNaRok, requiring O(t4), instead of the O(t3) possible for triplets). The method to quickly calculate triplets is applied to solving IterPCR (Pol and Escapa, 2009). It is shown that, in some cases, IterPCR or other algorithms in the program TNT (e.g. commands prunnelsen, prunmajor, or chkmoves) produce more informative results than analysis with RogueNaRok.
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científico y Técnicas. Centro Científico Tecnológico Tucumán. Unidad Ejecutora Lillo; Argentina
Fil: Szumik, Claudia Adriana. Consejo Nacional de Investigaciones Científico y Técnicas. Centro Científico Tecnológico Tucumán. Unidad Ejecutora Lillo; Argentina
description This paper describes an efficient implementation of triplet-based measures of stability, in the program TNT. The only available implementations of such measures are much slower than the present one, either because of an inefficient implementation (Phyutility, Thor) or because the stability is evaluated with quartets (RogueNaRok, requiring O(t4), instead of the O(t3) possible for triplets). The method to quickly calculate triplets is applied to solving IterPCR (Pol and Escapa, 2009). It is shown that, in some cases, IterPCR or other algorithms in the program TNT (e.g. commands prunnelsen, prunmajor, or chkmoves) produce more informative results than analysis with RogueNaRok.
publishDate 2015
dc.date.none.fl_str_mv 2015-07
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/12474
Goloboff, Pablo Augusto; Szumik, Claudia Adriana; Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok; Elsevier Inc; Molecular Phylogenetics And Evolution; 88; 7-2015; 93-104
1055-7903
url http://hdl.handle.net/11336/12474
identifier_str_mv Goloboff, Pablo Augusto; Szumik, Claudia Adriana; Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok; Elsevier Inc; Molecular Phylogenetics And Evolution; 88; 7-2015; 93-104
1055-7903
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1016/j.ympev.2015.04.003
info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1055790315000998
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier Inc
publisher.none.fl_str_mv Elsevier Inc
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.952241

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