Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM

Autores
Goloboff, Pablo Augusto
Año de publicación
2013
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Oblong, a program with very low memory requirements, is presented. It is designed for parsimony analysis of data sets comprising many characters for moderate numbers of taxa (the order of up to a few hundred). The program can avoid using vast amounts of RAM by temporarily saving data to disk buffers, only parts of which are periodically read back in by the program. In this way, the entire data set is never held in RAM by the program—only small parts of it. While using disk files to store the data slows down searches, it does so only by a relatively small factor (4× to 5×), because the program minimizes the number of times the data must be accessed (i.e. read back in) during tree searches. Thus, even if the program is not designed primarily for speed, runtimes are within an order of magnitude of those of the fastest existing parsimony programs.
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Instituto Superior de Entomología; Argentina
Materia
Cladistics
Parsimony
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/30210
Acceder
id CONICETDig_7597a5f5b31eff526b0f47c51ffaeb6c
oai_identifier_str oai:ri.conicet.gov.ar:11336/30210
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAMGoloboff, Pablo AugustoCladisticsParsimonyhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Oblong, a program with very low memory requirements, is presented. It is designed for parsimony analysis of data sets comprising many characters for moderate numbers of taxa (the order of up to a few hundred). The program can avoid using vast amounts of RAM by temporarily saving data to disk buffers, only parts of which are periodically read back in by the program. In this way, the entire data set is never held in RAM by the program—only small parts of it. While using disk files to store the data slows down searches, it does so only by a relatively small factor (4× to 5×), because the program minimizes the number of times the data must be accessed (i.e. read back in) during tree searches. Thus, even if the program is not designed primarily for speed, runtimes are within an order of magnitude of those of the fastest existing parsimony programs.Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Instituto Superior de Entomología; ArgentinaWiley2013-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/30210Goloboff, Pablo Augusto; Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM; Wiley; Cladistics; 30; 3; 9-2013; 273-2810748-3007CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1111/cla.12056info:eu-repo/semantics/altIdentifier/url/http://onlinelibrary.wiley.com/doi/10.1111/cla.12056/abstractinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:56:38Zoai:ri.conicet.gov.ar:11336/30210instacron: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:34982025-09-03 09:56:38.615CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM
title Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM
spellingShingle Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM
Goloboff, Pablo Augusto
Cladistics
Parsimony
title_short Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM
title_full Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM
title_fullStr Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM
title_full_unstemmed Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM
title_sort Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM
dc.creator.none.fl_str_mv Goloboff, Pablo Augusto
author Goloboff, Pablo Augusto
author_facet Goloboff, Pablo Augusto
author_role author
dc.subject.none.fl_str_mv Cladistics
Parsimony
topic Cladistics
Parsimony
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Oblong, a program with very low memory requirements, is presented. It is designed for parsimony analysis of data sets comprising many characters for moderate numbers of taxa (the order of up to a few hundred). The program can avoid using vast amounts of RAM by temporarily saving data to disk buffers, only parts of which are periodically read back in by the program. In this way, the entire data set is never held in RAM by the program—only small parts of it. While using disk files to store the data slows down searches, it does so only by a relatively small factor (4× to 5×), because the program minimizes the number of times the data must be accessed (i.e. read back in) during tree searches. Thus, even if the program is not designed primarily for speed, runtimes are within an order of magnitude of those of the fastest existing parsimony programs.
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Instituto Superior de Entomología; Argentina
description Oblong, a program with very low memory requirements, is presented. It is designed for parsimony analysis of data sets comprising many characters for moderate numbers of taxa (the order of up to a few hundred). The program can avoid using vast amounts of RAM by temporarily saving data to disk buffers, only parts of which are periodically read back in by the program. In this way, the entire data set is never held in RAM by the program—only small parts of it. While using disk files to store the data slows down searches, it does so only by a relatively small factor (4× to 5×), because the program minimizes the number of times the data must be accessed (i.e. read back in) during tree searches. Thus, even if the program is not designed primarily for speed, runtimes are within an order of magnitude of those of the fastest existing parsimony programs.
publishDate 2013
dc.date.none.fl_str_mv 2013-09
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/11336/30210
Goloboff, Pablo Augusto; Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM; Wiley; Cladistics; 30; 3; 9-2013; 273-281
0748-3007
CONICET Digital
CONICET
url http://hdl.handle.net/11336/30210
identifier_str_mv Goloboff, Pablo Augusto; Oblong, a program to analyse phylogenomic data sets with millions of characters, requiring negligible amounts of RAM; Wiley; Cladistics; 30; 3; 9-2013; 273-281
0748-3007
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1111/cla.12056
info:eu-repo/semantics/altIdentifier/url/http://onlinelibrary.wiley.com/doi/10.1111/cla.12056/abstract
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
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
_version_ 1842269415112966144
score 13.13397

Publicaciones similares