<scp>ggtree</scp> : an <scp>r</scp> package for visualization and annotation of phylogenetic trees with their covariates and other associated data

<jats:title>Summary</jats:title> <jats:p> <jats:list> <jats:list-item> <jats:p> We present an <jats:sc>r</jats:sc> package, <jats:sc>ggtree</jats:sc> , which provides programmable visualization and annotation of phylogenetic trees. </jats:p> </jats:list-item> <jats:list-item> <jats:p> <jats:sc>ggtree</jats:sc> can read more tree file formats than other softwares, including <jats:italic>newick</jats:italic> , <jats:italic>nexus</jats:italic> , <jats:italic>NHX</jats:italic> , <jats:italic>phylip</jats:italic> and <jats:italic>jplace</jats:italic> formats, and support visualization of <jats:italic>phylo, multiphylo, phylo4, phylo4d, obkdata</jats:italic> and <jats:italic>phyloseq</jats:italic> tree objects defined in other <jats:sc>r</jats:sc> packages. It can also extract the tree/branch/node‐specific and other data from the analysis outputs of <jats:sc>beast</jats:sc> , <jats:sc>epa</jats:sc> , <jats:sc>hyphy</jats:sc> , <jats:sc>paml</jats:sc> , <jats:sc>phylodog</jats:sc> , <jats:sc>pplacer</jats:sc> , <jats:sc>r8s</jats:sc> , <jats:sc>raxml</jats:sc> and <jats:sc>revbayes</jats:sc> software, and allows using these data to annotate the tree. </jats:p> </jats:list-item> <jats:list-item> <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> </jats:list-item> <jats:list-item> <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> </jats:list-item> <jats:list-item> <jats:p> The package <jats:sc>ggtree</jats:sc> is released under the <jats:sc>artistic‐2.0 license</jats:sc> . The source code and documents are freely available through <jats:sc>bioconductor</jats:sc> ( <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> ). </jats:p> </jats:list-item> </jats:list> </jats:p>