{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1363388845796359552.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1111/2041-210x.12628"}},{"identifier":{"@type":"URI","@value":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F2041-210X.12628"}},{"identifier":{"@type":"URI","@value":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12628"}},{"identifier":{"@type":"URI","@value":"https://onlinelibrary.wiley.com/doi/full-xml/10.1111/2041-210X.12628"}},{"identifier":{"@type":"URI","@value":"https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12628"}}],"dc:title":[{"@value":"<scp>ggtree</scp>\n                    : an\n                    <scp>r</scp>\n                    package for visualization and annotation of phylogenetic trees with their covariates and other associated data"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>Summary</jats:title>\n                  <jats:p>\n                    <jats:list>\n                      <jats:list-item>\n                        <jats:p>\n                          We present an\n                          <jats:sc>r</jats:sc>\n                          package,\n                          <jats:sc>ggtree</jats:sc>\n                          , which provides programmable visualization and annotation of phylogenetic trees.\n                        </jats:p>\n                      </jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\n                          <jats:sc>ggtree</jats:sc>\n                          can read more tree file formats than other softwares, including\n                          <jats:italic>newick</jats:italic>\n                          ,\n                          <jats:italic>nexus</jats:italic>\n                          ,\n                          <jats:italic>NHX</jats:italic>\n                          ,\n                          <jats:italic>phylip</jats:italic>\n                          and\n                          <jats:italic>jplace</jats:italic>\n                          formats, and support visualization of\n                          <jats:italic>phylo, multiphylo, phylo4, phylo4d, obkdata</jats:italic>\n                          and\n                          <jats:italic>phyloseq</jats:italic>\n                          tree objects defined in other\n                          <jats:sc>r</jats:sc>\n                          packages. It can also extract the tree/branch/node‐specific and other data from the analysis outputs of\n                          <jats:sc>beast</jats:sc>\n                          ,\n                          <jats:sc>epa</jats:sc>\n                          ,\n                          <jats:sc>hyphy</jats:sc>\n                          ,\n                          <jats:sc>paml</jats:sc>\n                          ,\n                          <jats:sc>phylodog</jats:sc>\n                          ,\n                          <jats:sc>pplacer</jats:sc>\n                          ,\n                          <jats:sc>r8s</jats:sc>\n                          ,\n                          <jats:sc>raxml</jats:sc>\n                          and\n                          <jats:sc>revbayes</jats:sc>\n                          software, and allows using these data to annotate the tree.\n                        </jats:p>\n                      </jats:list-item>\n                      <jats:list-item>\n                        <jats:p>The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion.</jats:p>\n                      </jats:list-item>\n                      <jats:list-item>\n                        <jats:p>A two‐dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images.</jats:p>\n                      </jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\n                          The package\n                          <jats:sc>ggtree</jats:sc>\n                          is released under the\n                          <jats:sc>artistic‐2.0 license</jats:sc>\n                          . The source code and documents are freely available through\n                          <jats:sc>bioconductor</jats:sc>\n                          (\n                          <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"http://www.bioconductor.org/packages/ggtree\">http://www.bioconductor.org/packages/ggtree</jats:ext-link>\n                          ).\n                        </jats:p>\n                      </jats:list-item>\n                    </jats:list>\n                  </jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1383388845796359554","@type":"Researcher","foaf:name":[{"@value":"Guangchuang Yu"}],"jpcoar:affiliationName":[{"@value":"State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China"}]},{"@id":"https://cir.nii.ac.jp/crid/1383388845796359424","@type":"Researcher","foaf:name":[{"@value":"David K. Smith"}],"jpcoar:affiliationName":[{"@value":"State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China"}]},{"@id":"https://cir.nii.ac.jp/crid/1383388845796359556","@type":"Researcher","foaf:name":[{"@value":"Huachen Zhu"}],"jpcoar:affiliationName":[{"@value":"State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China"}]},{"@id":"https://cir.nii.ac.jp/crid/1383388845796359553","@type":"Researcher","foaf:name":[{"@value":"Yi Guan"}],"jpcoar:affiliationName":[{"@value":"State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China"}]},{"@id":"https://cir.nii.ac.jp/crid/1383388845796359552","@type":"Researcher","foaf:name":[{"@value":"Tommy Tsan‐Yuk Lam"}],"jpcoar:affiliationName":[{"@value":"State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research School of Public Health The University of Hong Kong 21 Sassoon Road Pokfulam Hong Kong SAR China"}]}],"contributor":[{"@id":"https://cir.nii.ac.jp/crid/1383388845796359555","@type":"Researcher","foaf:name":[{"@value":"Greg McInerny"}],"role":"editor"}],"publication":{"publicationIdentifier":[{"@type":"PISSN","@value":"2041210X"},{"@type":"EISSN","@value":"2041210X"}],"prism:publicationName":[{"@value":"Methods in Ecology and Evolution"}],"dc:publisher":[{"@value":"Wiley"}],"prism:publicationDate":"2016-09-22","prism:volume":"8","prism:number":"1","prism:startingPage":"28","prism:endingPage":"36"},"reviewed":"false","dc:rights":["http://onlinelibrary.wiley.com/termsAndConditions#vor"],"url":[{"@id":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F2041-210X.12628"},{"@id":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12628"},{"@id":"https://onlinelibrary.wiley.com/doi/full-xml/10.1111/2041-210X.12628"},{"@id":"https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12628"}],"createdAt":"2016-08-16","modifiedAt":"2023-09-06","relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1050011495267167744","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"MIR2111-5 locus and shoot-accumulated mature miR2111 systemically enhance nodulation depending on HAR1 in Lotus 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Biwa"}]},{"@id":"https://cir.nii.ac.jp/crid/1360013168752625280","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion"}]},{"@id":"https://cir.nii.ac.jp/crid/1360013168773990144","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Termite dispersal is influenced by their diet"}]},{"@id":"https://cir.nii.ac.jp/crid/1360021390581724288","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Frequent nonhomologous replacement of replicative helicase loaders by viruses in\n            <i>Vibrionaceae</i>"}]},{"@id":"https://cir.nii.ac.jp/crid/1360021390739030784","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Potential 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phylogeny"}]},{"@id":"https://cir.nii.ac.jp/crid/1360022307168375040","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Emergence of rare carbapenemases (FRI, GES-5, IMI, SFC, and SFH-1) in Enterobacterales isolated from surface waters in Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1360025430192357248","@type":"Article","resourceType":"preprint","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Carotenoid pigments enhance rhodopsin-mediated phototrophy by light-harvesting and photocycle-accelerating"}]},{"@id":"https://cir.nii.ac.jp/crid/1360025430216732032","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"A nuclear genome assembly of an extinct flightless bird, the little bush moa"}]},{"@id":"https://cir.nii.ac.jp/crid/1360286995778005376","@type":"Article","resourceType":"学術雑誌論文(journal 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