Data from: ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

We 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).