Treehouse: a user-friendly application to obtain subtrees from large phylogenies
Related Experiment Video
Updated: Jan 20, 2026

A User-friendly and Powerful R Analysis of Large-scale Datasets
Published on: November 4, 2025
Jacob L Steenwyk1, Antonis Rokas2
1Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
Objective:
Phylogenetic trees that contain hundreds to thousands of taxa are now routinely generated. Retrieving the relationships among a subset of taxa in these large phylogenies can be a challenging or time-consuming task. Addressing this challenge requires the development of tools that facilitate the easy retrieval of subtrees from any user-specified set of taxa in a given phylogeny.
Results:
We developed treehouse, an open source tool that enables the retrieval of any subtree from a given large phylogeny. With a three-step workflow, treehouse successfully allows a user to obtain a subtree from any phylogeny. Treehouse can help researchers to explore the relationships among any set of taxa from across the tree of life. Treehouse is implemented as a shiny application in the R programming language. Treehouse software and usage instructions are publicly available at https://github.com/JLSteenwyk/treehouse .
More Related Videos
08:39High-throughput Image Analysis of Tumor Spheroids: A User-friendly Software Application to Measure the Size of Spheroids Automatically and Accurately
Published on: July 8, 2014
14:28Substructure Analyzer: A User-Friendly Workflow for Rapid Exploration and Accurate Analysis of Cellular Bodies in Fluorescence Microscopy Images
Published on: July 15, 2020
Related Concept Videos
Phylogeny
Photoluminescence: Applications
Radiation: Applications
The average...
Applications of Stress
The...
Environmental Applications of Microorganisms
Application of Linearization and Approximation