tanggle: An R package for the visualization of phylogenetic networks

Phylogenetic trees depict evolutionary relationships among taxa. However, they are strictly bifurcating structures that do not take into account several types of evolutionary events such as horizontal gene transfer, hybridization, or introgression. Although the development of new methods in phylogenetic networks has recently increased, limited visualization software is available to plot the phylogenetic networks.

Here, we present the R package tanggle, a visualization package for phylogenetic networks. Our package extends the widely used visualization package ggtree and allows a variety of input data from DNA sequences to extended Newick format; it also builds on the flexibility of ggplot2 to manipulate colors and other plot characteristics. In addition, our package allows for the inclusion of images and mapped morphological and geographical characteristics on the network.

In response to growing demands for reproducible, open-source research, tanggle facilitates the production of script-based, publication-quality figures rather than graphics manually created with design software. By embedding figure code and metadata directly within analysis pipelines, tanggle improves transparency, traceability, and version control; enables automated regeneration of figures as data or methods change; and simplifies sharing and reuse of visualizations.