PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods

Detalhes bibliográficos
Autor(a) principal: Nascimento, Marta
Data de Publicação: 2017
Outros Autores: Sousa, Adriano, Ramirez, Mario, Francisco, Alexandre, Carrico, Joao, Vaz, Cátia
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.21/7948
Resumo: High Throughput Sequencing provides a cost effective means of generating high resolution data for hundreds or even thousands of strains, and is rapidly superseding methodologies based on a few genomic loci. The wealth of genomic data deposited on public databases such as Sequence Read Archive/European Nucleotide Archive provides a powerful resource for evolutionary analysis and epidemiological surveillance. However, many of the analysis tools currently available do not scale well to these large datasets, nor provide the means to fully integrate ancillary data. Here we present PHYLOViZ 2.0, an extension of PHYLOViZ tool, a platform independent Java tool that allows phylogenetic inference and data visualization for large datasets of sequence based typing methods, including Single Nucleotide Polymorphism ( SNP) and whole genome/core genome Multilocus Sequence Typing (wg/cgMLST) analysis. PHYLOViZ 2.0 incorporates new data analysis algorithms and new visualization modules, as well as the capability of saving projects for subsequent work or for dissemination of results.
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spelling PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methodsTyping dataBacterialEburstToolsHigh Throughput Sequencing provides a cost effective means of generating high resolution data for hundreds or even thousands of strains, and is rapidly superseding methodologies based on a few genomic loci. The wealth of genomic data deposited on public databases such as Sequence Read Archive/European Nucleotide Archive provides a powerful resource for evolutionary analysis and epidemiological surveillance. However, many of the analysis tools currently available do not scale well to these large datasets, nor provide the means to fully integrate ancillary data. Here we present PHYLOViZ 2.0, an extension of PHYLOViZ tool, a platform independent Java tool that allows phylogenetic inference and data visualization for large datasets of sequence based typing methods, including Single Nucleotide Polymorphism ( SNP) and whole genome/core genome Multilocus Sequence Typing (wg/cgMLST) analysis. PHYLOViZ 2.0 incorporates new data analysis algorithms and new visualization modules, as well as the capability of saving projects for subsequent work or for dissemination of results.Oxford University PressRCIPLNascimento, MartaSousa, AdrianoRamirez, MarioFrancisco, AlexandreCarrico, JoaoVaz, Cátia2018-01-19T11:30:37Z2017-012017-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.21/7948engNASCIMENTO, Marta; [et al] – PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. Bioinformatics. ISSN 1367-4803. Vol. 33, N.º 1 (2017), pp. 128-1291367-480310.1093/bioinformatics/btw582metadata only accessinfo: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:RCAAP2023-08-03T09:54:43Zoai:repositorio.ipl.pt:10400.21/7948Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T20:16:48.098193Repositório 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 PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
title PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
spellingShingle PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
Nascimento, Marta
Typing data
Bacterial
Eburst
Tools
title_short PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
title_full PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
title_fullStr PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
title_full_unstemmed PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
title_sort PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
author Nascimento, Marta
author_facet Nascimento, Marta
Sousa, Adriano
Ramirez, Mario
Francisco, Alexandre
Carrico, Joao
Vaz, Cátia
author_role author
author2 Sousa, Adriano
Ramirez, Mario
Francisco, Alexandre
Carrico, Joao
Vaz, Cátia
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv RCIPL
dc.contributor.author.fl_str_mv Nascimento, Marta
Sousa, Adriano
Ramirez, Mario
Francisco, Alexandre
Carrico, Joao
Vaz, Cátia
dc.subject.por.fl_str_mv Typing data
Bacterial
Eburst
Tools
topic Typing data
Bacterial
Eburst
Tools
description High Throughput Sequencing provides a cost effective means of generating high resolution data for hundreds or even thousands of strains, and is rapidly superseding methodologies based on a few genomic loci. The wealth of genomic data deposited on public databases such as Sequence Read Archive/European Nucleotide Archive provides a powerful resource for evolutionary analysis and epidemiological surveillance. However, many of the analysis tools currently available do not scale well to these large datasets, nor provide the means to fully integrate ancillary data. Here we present PHYLOViZ 2.0, an extension of PHYLOViZ tool, a platform independent Java tool that allows phylogenetic inference and data visualization for large datasets of sequence based typing methods, including Single Nucleotide Polymorphism ( SNP) and whole genome/core genome Multilocus Sequence Typing (wg/cgMLST) analysis. PHYLOViZ 2.0 incorporates new data analysis algorithms and new visualization modules, as well as the capability of saving projects for subsequent work or for dissemination of results.
publishDate 2017
dc.date.none.fl_str_mv 2017-01
2017-01-01T00:00:00Z
2018-01-19T11:30:37Z
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/10400.21/7948
url http://hdl.handle.net/10400.21/7948
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv NASCIMENTO, Marta; [et al] – PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. Bioinformatics. ISSN 1367-4803. Vol. 33, N.º 1 (2017), pp. 128-129
1367-4803
10.1093/bioinformatics/btw582
dc.rights.driver.fl_str_mv metadata only access
info:eu-repo/semantics/openAccess
rights_invalid_str_mv metadata only access
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University 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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