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

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…

• UO
  University of Hong Kong

  Award: 201411159214
• WR
  Walter Reed Army Institute of Research