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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Publications at this Location » Publication #434432
Research Project: Knowledge Based Tools for Exotic and Emerging Diseases of Small Fruit and Nursery Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

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

Author
item Foster, Zachary
item CHANG, JEFF - Oregon State University
item Grunwald, Niklaus

Submitted to: ArXiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 5/4/2026
Publication Date: 5/4/2026
Citation: Foster, Z.S.L., Chang, J.H., Grünwald, N.J. 2026. Heat-tree: Cross-platform software for interactive and embeddable phylogenetic tree visualization and editing. ArXiv. https://doi.org/10.48550/arXiv.2605.01109.
DOI: https://doi.org/10.48550/arXiv.2605.01109

Interpretive Summary: Phylogenetic trees are tool fundamental to understanding the evolution and genetics of organisms and their genetic data. While many tools exist for tree visualization, most are limited to static graphics or require significant coding expertise. We introduce heattree, a software package ecosystem that enables interactive visualization and manipulation of phylogenetic trees with associated exploratory data. These new tools allow creation of customizable, web-compatible tree visualizations. heattree is unique in its ability to function as a tree viewer, editor, and self-contained, embeddable visualization.

Technical Abstract: Phylogenetic trees are fundamental tools in evolutionary biology, genomics, and ecology. While many tools exist for phylogenetic tree visualization, most are limited to static graphics, require significant coding expertise to use, or are bespoke solutions for a specific website. We introduce heattree, a software package ecosystem consisting of a JavaScript library and both Python and R packages that enable interactive visualization and manipulation of phylogenetic trees with associated metadata. The heattree packages allow creation of customizable, web-compatible tree visualizations that can be embedded in Markdown, Jupyter, and Quarto documents, as well as directly in HTML/JavaScript applications. The package supports radial and rectangular tree layouts, mapping metadata to visual aesthetics, interactive tree editing, and export capabilities for publication-quality figures. heattree is unique in its ability to function as a tree viewer, editor, and self-contained, embeddable visualization.