treeio

treeio parses, stores, and exports phylogenetic trees and their associated heterogeneous data to enable integration and downstream comparative and visualization analyses.

Key Features:

• Parsing and Exporting: Extraction and export of phylogenetic trees and associated annotations from a variety of analytical software outputs.
• Data Integration: Linking of external datasets to phylogenies and merging of tree data from multiple sources to associate heterogeneous metadata with tree structures.
• Export Capabilities: Export of phylogenetic trees and associated data into cohesive file formats, including BEAST-compatible NEXUS and jtree formats.
• Compatibility and Interoperability: Interoperation with the tidytree and ggtree packages to enable tidy-format processing and advanced tree visualization workflows.

Scientific Applications:

• Comparative Studies: Integration of results from diverse phylogenetic analyses to support comparative evolutionary investigations.
• Data Sharing and Conversion: Conversion and export to multiple formats to facilitate data exchange and reuse in downstream analyses.
• Interdisciplinary Analysis: Association of external biological datasets with phylogenies to support evolutionary interpretation across disciplines.

Methodology:

Implementation of base classes and functions that standardize parsing and exporting of phylogenetic trees and associated data, with integration into the Bioconductor and rOpenSci ecosystems.