Heat-tree: Cross-platform software for interactive and embeddable phylogenetic tree visualization and editing

TL;DR

Heat-tree is a versatile, cross-platform software suite in JavaScript, R, and Python that enables interactive, customizable, and embeddable visualization and editing of phylogenetic trees and metadata.

Contribution

It introduces a user-friendly, extensible toolset for interactive phylogenetic tree visualization and editing across multiple programming environments.

Findings

Supports radial and rectangular layouts

Enables automated metadata encoding into visual features

Allows export of publication-quality figures

Abstract

Phylogenetic trees are the primary framework for conveying evolutionary relationships. While many tools exist for visualizing phylogenetic trees, most are limited to static graphics, require coding expertise, or are developed for a specific website and not easily reusable or extensible. To address these limitations, we developed heat-tree, a collection of software packages in JavaScript, R, and Python for interactive visualization, manipulation, and editing of phylogenetic trees and their associated metadata. Heat-tree allows for the creation of customizable, web-compatible tree visualizations that can be easily embedded in R Markdown, Jupyter Notebooks, and Quarto documents, as well as directly in HTML/JavaScript applications and websites. The package supports radial and rectangular tree layouts, automated translation of metadata values into visual encodings on the tree, interactive tree editing, and export capabilities for publication-quality figures. All visualization parameters are definable programmatically or interactively using the comprehensive graphical user interface included with each visualization. Heat-tree was designed to be a user-friendly software package for interactive tree viewing, manipulation, editing, and self-contained, embeddable visualization across software environments.