Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

Area of Science:

• Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• Phylogenetic trees and associated data are frequently stored in incompatible formats.
• Integrating results from different phylogenetic software is challenging due to format inconsistencies.

Purpose of the Study:

• To introduce the treeio R package for seamless integration of phylogenetic tree data.
• To enable linking and merging of diverse phylogenetic datasets for comprehensive analysis.

Main Methods:

• The treeio package supports reading and writing various phylogenetic tree formats.
• It facilitates the extraction and linking of external data to phylogenetic trees.
• The package enables merging of tree data from multiple sources.

Main Results:

• treeio provides a unified interface for handling phylogenetic trees and associated data.
• It supports export to common formats like NEXUS and jtree for data sharing.
• The package integrates with tidytree and ggtree for data processing and visualization.

Conclusions:

• treeio enhances the interoperability of phylogenetic data, simplifying comparative evolutionary studies.
• It promotes data sharing and reproducible research in evolutionary biology and related fields.