Gene

Engineering

Biology

Statistics

Visualization

Node (physics)

R package

Biochemistry

Data mining

Computer science

Computational biology

Zoom

Evolutionary biology

Paleontology

Genetics

Phylogenetic tree

Lens (geology)

Bioinformatics

Mathematics

Phylogenetics

Mathematical analysis

Artificial intelligence

Tree (set theory)

Structural engineering

Machine learning

Covariate

Annotation

Bioconductor

Methods in Ecology and Evolution

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).

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

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