GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

Detalhes bibliográficos
Autor(a) principal: Zhou, Zhemin
Data de Publicação: 2018
Outros Autores: Alikhan, Nabil-Fareed, Sergeant, Martin, Luhmann, Nina, Vaz, Cátia, Francisco, Alexandre, Carrico, Joao, Achtman, Mark
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.21/9099
Resumo: Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.
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spelling GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogensBacterial genomeGrapeTreeGenoma bacterianoCurrent methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.Cold Spring Harbor Laboratory PressRCIPLZhou, ZheminAlikhan, Nabil-FareedSergeant, MartinLuhmann, NinaVaz, CátiaFrancisco, AlexandreCarrico, JoaoAchtman, Mark2018-11-28T11:56:44Z2018-092018-09-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.21/9099engZHEMIN, Zhou; [et al] – GrapeTree visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Research. ISSN 1088-9051. Vol. 28, N.º 9 (2018), pp. 1395-14041088-905110.1101/gr.232397.117info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-08-03T09:57:23Zoai:repositorio.ipl.pt:10400.21/9099Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T20:17:44.631837Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
spellingShingle GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
Zhou, Zhemin
Bacterial genome
GrapeTree
Genoma bacteriano
title_short GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title_full GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title_fullStr GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title_full_unstemmed GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title_sort GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
author Zhou, Zhemin
author_facet Zhou, Zhemin
Alikhan, Nabil-Fareed
Sergeant, Martin
Luhmann, Nina
Vaz, Cátia
Francisco, Alexandre
Carrico, Joao
Achtman, Mark
author_role author
author2 Alikhan, Nabil-Fareed
Sergeant, Martin
Luhmann, Nina
Vaz, Cátia
Francisco, Alexandre
Carrico, Joao
Achtman, Mark
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv RCIPL
dc.contributor.author.fl_str_mv Zhou, Zhemin
Alikhan, Nabil-Fareed
Sergeant, Martin
Luhmann, Nina
Vaz, Cátia
Francisco, Alexandre
Carrico, Joao
Achtman, Mark
dc.subject.por.fl_str_mv Bacterial genome
GrapeTree
Genoma bacteriano
topic Bacterial genome
GrapeTree
Genoma bacteriano
description Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.
publishDate 2018
dc.date.none.fl_str_mv 2018-11-28T11:56:44Z
2018-09
2018-09-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10400.21/9099
url http://hdl.handle.net/10400.21/9099
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv ZHEMIN, Zhou; [et al] – GrapeTree visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Research. ISSN 1088-9051. Vol. 28, N.º 9 (2018), pp. 1395-1404
1088-9051
10.1101/gr.232397.117
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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