ggtree

ggtree visualizes and annotates phylogenetic trees to integrate structural and associated biological data for evolutionary and comparative analyses.

Key Features:

• Grammar of Graphics (ggplot2 integration): Implements the ggplot2 grammar of graphics to provide programmable tree plotting and layered annotations.
• Extensive Format Support: Parses tree file formats Newick, Nexus, NHX, Phylip, and Jplace.
• Integration with R Packages: Accepts tree objects from phylo, multiphylo, phylo4, phylo4d, obkdata, and phyloseq.
• Data Extraction from Analytical Software: Extracts tree-, branch-, and node-specific data from BEAST, EPA, HyPhy, PAML, PhyloDogg, pplacer, r8s, RAxML, and RevBayes outputs.
• Advanced Visualization Operations: Supports coloring and annotation by numerical or categorical node attributes, rotating, collapsing, zooming clades, and highlighting selected clades or operational taxonomic units.
• Two-Dimensional Tree Scaling: Draws two-dimensional trees with width scaled according to node attributes.
• Annotation with Associated Data: Annotates trees with associated numerical matrices (e.g., heat maps), multiple sequence alignments, subplots, and silhouette images.

Scientific Applications:

• Evolutionary biology visualization: Enables visualization and annotation of complex phylogenetic relationships for evolutionary analyses.
• Integration of phylogenetic outputs: Facilitates integration and interpretation of outputs from software such as BEAST, RAxML, pplacer, and RevBayes for comprehensive phylogenetic analysis.

Methodology:

Implements the ggplot2 grammar of graphics for programmable visualizations and parses tree file formats (Newick, Nexus, NHX, Phylip, Jplace) and tree objects (phylo, multiphylo, phylo4, phylo4d, obkdata, phyloseq) while extracting node and branch data from BEAST, EPA, HyPhy, PAML, PhyloDogg, pplacer, r8s, RAxML, and RevBayes.