Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2018 |
| Outros Autores: | , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Institucional da UFMG |
| Texto Completo: | http://dx.doi.org/10.7717/peerj.4349 http://hdl.handle.net/1843/55174 https://orcid.org/0000-0002-7692-6243 https://orcid.org/0000-0003-1772-7727 https://orcid.org/0000-0001-6590-4287 https://orcid.org/0000-0002-0053-3574 https://orcid.org/0000-0001-7446-1342 https://orcid.org/0000-0002-8667-9530 https://orcid.org/0000-0003-1404-3485 https://orcid.org/0000-0002-2308-3983 https://orcid.org/0000-0002-9323-1400 |
Resumo: | CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico |
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2023-06-20T19:30:02Z2023-06-20T19:30:02Z20186e4349http://dx.doi.org/10.7717/peerj.43492167-8359http://hdl.handle.net/1843/55174https://orcid.org/0000-0002-7692-6243https://orcid.org/0000-0003-1772-7727https://orcid.org/0000-0001-6590-4287https://orcid.org/0000-0002-0053-3574https://orcid.org/0000-0001-7446-1342https://orcid.org/0000-0002-8667-9530https://orcid.org/0000-0003-1404-3485https://orcid.org/0000-0002-2308-3983https://orcid.org/0000-0002-9323-1400CNPq - Conselho Nacional de Desenvolvimento Científico e TecnológicoComplex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.engUniversidade Federal de Minas GeraisUFMGBrasilICB - DEPARTAMENTO DE MICROBIOLOGIAPeerJRedes complexasFilogeniaBasidiomycotaQuitina sintaseComplex networksCommunity detectionPhylogenetic methodsStatistical supportBasidiomycotaChitin synthasesComparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap methodComparação de redes complexas e métodos baseados em árvores de análise filogenética e proposta de um método bootstrapinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttps://peerj.com/articles/4349/#p-1Aristóteles Góes-NetoMarcelo V.C. DinizDaniel Santana de CarvalhoGilberto Cafezeiro BomfimAngelo Amâncio DuarteJerzy A. BrzozowskiThierry C. Petit LobãoSuani T.R. PinhoCharbel N. El-HaniRoberto Fernandes Silva Andradeapplication/pdfinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFMGinstname:Universidade Federal de Minas Gerais (UFMG)instacron:UFMGLICENSELicense.txtLicense.txttext/plain; charset=utf-82042https://repositorio.ufmg.br/bitstream/1843/55174/1/License.txtfa505098d172de0bc8864fc1287ffe22MD51ORIGINALComparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method.pdfComparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method.pdfapplication/pdf1427866https://repositorio.ufmg.br/bitstream/1843/55174/2/Comparison%20of%20complex%20networks%20and%20tree-based%20methods%20of%20phylogenetic%20analysis%20and%20proposal%20of%20a%20bootstrap%20method.pdf0572967f8fbebbbc11e58342cc2d40c0MD521843/551742023-06-20 16:30:02.763oai:repositorio.ufmg.br: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Repositório de PublicaçõesPUBhttps://repositorio.ufmg.br/oaiopendoar:2023-06-20T19:30:02Repositório Institucional da UFMG - Universidade Federal de Minas Gerais (UFMG)false |
| dc.title.pt_BR.fl_str_mv |
Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method |
| dc.title.alternative.pt_BR.fl_str_mv |
Comparação de redes complexas e métodos baseados em árvores de análise filogenética e proposta de um método bootstrap |
| title |
Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method |
| spellingShingle |
Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method Aristóteles Góes-Neto Complex networks Community detection Phylogenetic methods Statistical support Basidiomycota Chitin synthases Redes complexas Filogenia Basidiomycota Quitina sintase |
| title_short |
Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method |
| title_full |
Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method |
| title_fullStr |
Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method |
| title_full_unstemmed |
Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method |
| title_sort |
Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method |
| author |
Aristóteles Góes-Neto |
| author_facet |
Aristóteles Góes-Neto Marcelo V.C. Diniz Daniel Santana de Carvalho Gilberto Cafezeiro Bomfim Angelo Amâncio Duarte Jerzy A. Brzozowski Thierry C. Petit Lobão Suani T.R. Pinho Charbel N. El-Hani Roberto Fernandes Silva Andrade |
| author_role |
author |
| author2 |
Marcelo V.C. Diniz Daniel Santana de Carvalho Gilberto Cafezeiro Bomfim Angelo Amâncio Duarte Jerzy A. Brzozowski Thierry C. Petit Lobão Suani T.R. Pinho Charbel N. El-Hani Roberto Fernandes Silva Andrade |
| author2_role |
author author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Aristóteles Góes-Neto Marcelo V.C. Diniz Daniel Santana de Carvalho Gilberto Cafezeiro Bomfim Angelo Amâncio Duarte Jerzy A. Brzozowski Thierry C. Petit Lobão Suani T.R. Pinho Charbel N. El-Hani Roberto Fernandes Silva Andrade |
| dc.subject.por.fl_str_mv |
Complex networks Community detection Phylogenetic methods Statistical support Basidiomycota Chitin synthases |
| topic |
Complex networks Community detection Phylogenetic methods Statistical support Basidiomycota Chitin synthases Redes complexas Filogenia Basidiomycota Quitina sintase |
| dc.subject.other.pt_BR.fl_str_mv |
Redes complexas Filogenia Basidiomycota Quitina sintase |
| description |
CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico |
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2018 |
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2018 |
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2023-06-20T19:30:02Z |
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2023-06-20T19:30:02Z |
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http://hdl.handle.net/1843/55174 |
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http://dx.doi.org/10.7717/peerj.4349 |
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2167-8359 |
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Universidade Federal de Minas Gerais |
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