GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT

Autores
Goloboff, Pablo Augusto; Catalano, Santiago Andres
Año de publicación
2012
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
This paper presents a pipeline, implemented in an open-source program called GB→TNT (GenBank-to-TNT), for creating large molecular matrices, starting from GenBank files and finishing with TNT matrices which incorporate taxonomic information in the terminal names. GB→TNT is designed to retrieve a defined genomic region from a bulk of sequences included in a GenBank file. The user defines the genomic region to be retrieved and several filters (genome, length of the sequence, taxonomic group, etc.); each genomic region represents a different data block in the final TNT matrix. GB→TNT first generates Fasta files from the input GenBank files, then creates an alignment for each of those (by calling an alignment program), and finally merges all the aligned files into a single TNT matrix. The new version of TNT can make use of the taxonomic information contained in the terminal names, allowing easy diagnosis of results, evaluation of fit between the trees and the taxonomy, and automatic labelling or colouring of tree branches with the taxonomic groups they represent. © The Willi Hennig Society 2012.
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentina
Fil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentina
Materia
Phylogeny Software
Genbank
Matrix Generation
Tnt
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:11336/60761
Acceder
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spelling GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNTGoloboff, Pablo AugustoCatalano, Santiago AndresPhylogeny SoftwareGenbankMatrix GenerationTnthttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1This paper presents a pipeline, implemented in an open-source program called GB→TNT (GenBank-to-TNT), for creating large molecular matrices, starting from GenBank files and finishing with TNT matrices which incorporate taxonomic information in the terminal names. GB→TNT is designed to retrieve a defined genomic region from a bulk of sequences included in a GenBank file. The user defines the genomic region to be retrieved and several filters (genome, length of the sequence, taxonomic group, etc.); each genomic region represents a different data block in the final TNT matrix. GB→TNT first generates Fasta files from the input GenBank files, then creates an alignment for each of those (by calling an alignment program), and finally merges all the aligned files into a single TNT matrix. The new version of TNT can make use of the taxonomic information contained in the terminal names, allowing easy diagnosis of results, evaluation of fit between the trees and the taxonomy, and automatic labelling or colouring of tree branches with the taxonomic groups they represent. © The Willi Hennig Society 2012.Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaFil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaWiley Blackwell Publishing, Inc2012-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/60761Goloboff, Pablo Augusto; Catalano, Santiago Andres; GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT; Wiley Blackwell Publishing, Inc; Cladistics; 28; 5; 4-2012; 503-5130748-3007CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1111/j.1096-0031.2012.00400.xinfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1096-0031.2012.00400.xinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:36:18Zoai:ri.conicet.gov.ar:11336/60761instacron: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:34982025-09-29 09:36:19.054CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT
title GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT
spellingShingle GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT
Goloboff, Pablo Augusto
Phylogeny Software
Genbank
Matrix Generation
Tnt
title_short GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT
title_full GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT
title_fullStr GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT
title_full_unstemmed GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT
title_sort GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT
dc.creator.none.fl_str_mv Goloboff, Pablo Augusto
Catalano, Santiago Andres
author Goloboff, Pablo Augusto
author_facet Goloboff, Pablo Augusto
Catalano, Santiago Andres
author_role author
author2 Catalano, Santiago Andres
author2_role author
dc.subject.none.fl_str_mv Phylogeny Software
Genbank
Matrix Generation
Tnt
topic Phylogeny Software
Genbank
Matrix Generation
Tnt
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 presents a pipeline, implemented in an open-source program called GB→TNT (GenBank-to-TNT), for creating large molecular matrices, starting from GenBank files and finishing with TNT matrices which incorporate taxonomic information in the terminal names. GB→TNT is designed to retrieve a defined genomic region from a bulk of sequences included in a GenBank file. The user defines the genomic region to be retrieved and several filters (genome, length of the sequence, taxonomic group, etc.); each genomic region represents a different data block in the final TNT matrix. GB→TNT first generates Fasta files from the input GenBank files, then creates an alignment for each of those (by calling an alignment program), and finally merges all the aligned files into a single TNT matrix. The new version of TNT can make use of the taxonomic information contained in the terminal names, allowing easy diagnosis of results, evaluation of fit between the trees and the taxonomy, and automatic labelling or colouring of tree branches with the taxonomic groups they represent. © The Willi Hennig Society 2012.
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentina
Fil: Catalano, Santiago Andres. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentina
description This paper presents a pipeline, implemented in an open-source program called GB→TNT (GenBank-to-TNT), for creating large molecular matrices, starting from GenBank files and finishing with TNT matrices which incorporate taxonomic information in the terminal names. GB→TNT is designed to retrieve a defined genomic region from a bulk of sequences included in a GenBank file. The user defines the genomic region to be retrieved and several filters (genome, length of the sequence, taxonomic group, etc.); each genomic region represents a different data block in the final TNT matrix. GB→TNT first generates Fasta files from the input GenBank files, then creates an alignment for each of those (by calling an alignment program), and finally merges all the aligned files into a single TNT matrix. The new version of TNT can make use of the taxonomic information contained in the terminal names, allowing easy diagnosis of results, evaluation of fit between the trees and the taxonomy, and automatic labelling or colouring of tree branches with the taxonomic groups they represent. © The Willi Hennig Society 2012.
publishDate 2012
dc.date.none.fl_str_mv 2012-04
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/11336/60761
Goloboff, Pablo Augusto; Catalano, Santiago Andres; GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT; Wiley Blackwell Publishing, Inc; Cladistics; 28; 5; 4-2012; 503-513
0748-3007
CONICET Digital
CONICET
url http://hdl.handle.net/11336/60761
identifier_str_mv Goloboff, Pablo Augusto; Catalano, Santiago Andres; GB-to-TNT: Facilitating creation of matrices from GenBank and diagnosis of results in TNT; Wiley Blackwell Publishing, Inc; Cladistics; 28; 5; 4-2012; 503-513
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/j.1096-0031.2012.00400.x
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1096-0031.2012.00400.x
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
application/pdf
dc.publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
publisher.none.fl_str_mv Wiley Blackwell Publishing, 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 13.070432

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