tanggle: An R package for the visualization of phylogenetic networks.

Area of Science:

• Evolutionary biology
• Bioinformatics
• Computational biology

Background:

• Phylogenetic trees are limited to bifurcating structures, failing to represent complex evolutionary events like horizontal gene transfer or hybridization.
• Existing visualization software for phylogenetic networks is limited, despite advancements in network methods.

Purpose of the Study:

• To introduce tanggle, an R package designed for visualizing phylogenetic networks.
• To provide a flexible and user-friendly tool for researchers studying complex evolutionary relationships.

Main Methods:

• tanggle extends the ggtree R package, leveraging ggplot2 for customizable plot aesthetics.
• The package accepts diverse input data, including DNA sequences and extended Newick formats.
• It supports the integration of images and mapped morphological/geographical data onto phylogenetic networks.

Main Results:

• tanggle enables the creation of publication-quality phylogenetic network visualizations.
• The package facilitates script-based figure generation, improving reproducibility and traceability.
• It allows for automated regeneration of figures as data or methods evolve.

Conclusions:

• tanggle addresses the need for advanced visualization tools in phylogenetic network analysis.
• The package enhances transparency, traceability, and version control in research workflows.
• tanggle simplifies the sharing and reuse of complex evolutionary visualizations.