DOI: 10.1111/2041-210x.12628 ISSN:

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

Guangchuang Yu, David K. Smith, Huachen Zhu, Yi Guan, Tommy Tsan‐Yuk Lam
  • Ecological Modeling
  • Ecology, Evolution, Behavior and Systematics
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Summary

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).

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