{"name":"ggtree","description":"Extend the 'ggplot2' plotting system which implemented the grammar of graphics. It is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.","homepage":"http://bioconductor.org/packages/release/bioc/html/ggtree.html","biotoolsID":"ggtree","biotoolsCURIE":"biotools:ggtree","version":["1.6.6"],"otherID":[],"relation":[],"function":[{"operation":[{"uri":"http://edamontology.org/operation_0567","term":"Phylogenetic tree visualisation"},{"uri":"http://edamontology.org/operation_0558","term":"Phylogenetic tree annotation"}],"input":[{"data":{"uri":"http://edamontology.org/data_0872","term":"Phylogenetic tree"},"format":[{"uri":"http://edamontology.org/format_2006","term":"Phylogenetic tree format"},{"uri":"http://edamontology.org/format_1912","term":"Nexus format"},{"uri":"http://edamontology.org/format_1435","term":"Phylip tree format"},{"uri":"http://edamontology.org/format_1910","term":"newick"}]}],"output":[{"data":{"uri":"http://edamontology.org/data_0872","term":"Phylogenetic tree"},"format":[{"uri":"http://edamontology.org/format_2006","term":"Phylogenetic tree format"},{"uri":"http://edamontology.org/format_3547","term":"Image format"}]},{"data":{"uri":"http://edamontology.org/data_1707","term":"Phylogenetic tree image"},"format":[{"uri":"http://edamontology.org/format_2006","term":"Phylogenetic tree format"},{"uri":"http://edamontology.org/format_3547","term":"Image format"}]}],"note":null,"cmd":null}],"toolType":["Command-line tool","Library"],"topic":[{"uri":"http://edamontology.org/topic_0084","term":"Phylogeny"},{"uri":"http://edamontology.org/topic_0092","term":"Data visualisation"}],"operatingSystem":["Linux","Windows","Mac"],"language":["R"],"license":"Artistic-2.0","collectionID":["BioConductor"],"maturity":null,"cost":null,"accessibility":null,"elixirPlatform":[],"elixirNode":[],"elixirCommunity":[],"link":[{"url":"https://guangchuangyu.github.io/ggtree","type":["Mirror"],"note":null}],"download":[{"url":"http://bioconductor/packages/release/bioc/src/contrib/ggtree_1.6.6.tar.gz","type":"Source code","note":null,"version":null}],"documentation":[{"url":"http://bioconductor.org/packages/release/bioc/html/ggtree.html","type":["User manual"],"note":null}],"publication":[{"doi":"10.1111/2041-210X.12628","pmid":null,"pmcid":null,"type":["Primary"],"version":null,"note":null,"metadata":{"title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","abstract":"© 2016 The Authors. Methods in Ecology and Evolution © 2016 British Ecological SocietyWe present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree. 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. 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. The package ggtree is released under the artistic-2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).","date":"2017-01-01T00:00:00Z","citationCount":951,"authors":[{"name":"Yu G."},{"name":"Smith D.K."},{"name":"Zhu H."},{"name":"Guan Y."},{"name":"Lam T.T.-Y."}],"journal":"Methods in Ecology and Evolution"}}],"credit":[{"name":"Guangchuang Yu","email":"guangchuangyu@gmail.com","url":null,"orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":"Person","typeRole":["Primary contact"],"note":null}],"owner":"bioconductor_import","additionDate":"2017-01-17T14:55:53Z","lastUpdate":"2018-12-10T12:58:54Z","editPermission":{"type":"private","authors":[]},"validated":1,"homepage_status":0,"elixir_badge":0,"confidence_flag":null}