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Related Experiment Video

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A User-friendly and Powerful R Analysis of Large-scale Datasets
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Treehouse: a user-friendly application to obtain subtrees from large phylogenies.

Jacob L Steenwyk1, Antonis Rokas2

  • 1Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.

BMC Research Notes
|August 29, 2019
PubMed
Summary

Researchers can now easily extract specific subtrees from large phylogenetic trees using treehouse, an open-source R tool. This facilitates exploring evolutionary relationships among selected taxa across the tree of life.

Keywords:
Big dataGraphical user interfacePhylogeneticsPhylogenomicsShinyTreeTree pruning

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Area of Science:

  • Evolutionary Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Phylogenetic trees with thousands of taxa are increasingly common.
  • Extracting relationships for specific taxa from large phylogenies is difficult.

Purpose of the Study:

  • To develop a tool for easily retrieving subtrees from large phylogenetic trees.
  • To enable researchers to explore evolutionary relationships among selected taxa.

Main Methods:

  • Developed treehouse, an open-source tool implemented as a Shiny application in R.
  • Utilized a three-step workflow for subtree retrieval.

Main Results:

  • treehouse successfully enables users to obtain any subtree from a given large phylogeny.
  • The tool facilitates exploration of taxon relationships across the tree of life.

Conclusions:

  • treehouse provides an efficient solution for navigating complex phylogenetic datasets.
  • The tool is publicly available for researchers to use and explore evolutionary insights.