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bioRxiv · 10.64898/2025.12.01.691494

Tree Explorer (T-REX): Bridging Phylogenetic and Phenotypic Data for Enhanced Analysis and Interpretation

Magill, D.·Ladriere, J.-M.
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Abstract

BackgroundThe Tree Explorer (T-REX) project is an open-source initiative designed to enhance the visualization and integration of phylogenetic and phenotypic data. Utilizing the ete3 toolkit, T-REX offers a user-friendly interface and a suite of tools written in Python. This project addresses the longstanding need to easily label phylogenetic trees with phenotypic data stored in other files and efficiently query this data to find entities of interest. ResultsT-REX includes various tools to help users prepare their input files and refine the output to create publication-worthy figures. It aims to facilitate the rapid identification of strains of interest for research projects, making large phylogenetic trees more interpretable and useful for evolutionary biology studies. ConclusionsT-REX provides an easy-to-use tool that allows users to effectively link their phylogenetic and phenotypic datasets in order to answer diverse biological questions. Available as a pre-compiled binary or rapid install, users can label trees, perform complex queries to identify individuals of interest, link large-scale quantitative datasets, and produce publication-ready figures. This tool, along with its future developments, is expected to assist in evolutionary biological studies and in the identification and selection of biological entities exhibiting traits of interest.

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Magill, D., Ladriere, J.-M.. 2025-12-02. Tree Explorer (T-REX): Bridging Phylogenetic and Phenotypic Data for Enhanced Analysis and Interpretation. https://doi.org/10.64898/2025.12.01.691494

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