treeio

Treeio is a software package that addresses the issue of incompatible and inconsistent formats in phylogenetic trees and data. It enables the extraction and integration of phylogenetic trees and outputs from various analytical software tools, allowing for comparative studies and merging tree data from different sources. Treeio also facilitates linking external data to phylogenies, enabling analyses of phylogeny-associated data from various disciplines in an evolutionary context.

The package supports the export of phylogenetic trees with heterogeneous-associated data to a single tree file, including BEAST-compatible NEXUS and jtree formats, promoting data sharing and file format conversion for downstream analysis. Treeio is designed to work seamlessly with the tidytree and ggtree packages, enabling tree data processing using the tidy interface and visualization through ggtree.