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OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life.

Emily Jane Mctavish1, Luna Luisa Sánchez-Reyes1, Mark T Holder2,3

  • 1Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA.

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The Open Tree of Life project offers a dynamic, digital tree of life using phylogenetic data. A new Python package, opentree, simplifies accessing and analyzing this evolutionary data for researchers.

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Area of Science:

  • Evolutionary Biology
  • Computational Biology
  • Biodiversity Informatics

Background:

  • The Open Tree of Life project aims to synthesize global phylogenetic information.
  • Existing phylogenetic data is often fragmented and difficult to access.
  • Web-service APIs are available for accessing the Open Tree of Life data.

Purpose of the Study:

  • To introduce the Python package 'opentree' as a user-friendly interface to Open Tree of Life APIs.
  • To facilitate downstream phylogenetic analyses using readily available data.
  • To demonstrate the utility of 'opentree' with real-world case studies.

Main Methods:

  • Development of the Python package 'opentree' as a wrapper for Open Tree of Life APIs.
  • Utilization of scripts and tutorials for data analysis.
  • Application of the tools to generate phylogenetic estimates for bird families and local biodiversity.

Main Results:

  • The 'opentree' Python package provides accessible tools for phylogenetic analysis.
  • Successful generation of a phylogenetic estimate for all bird families.
  • Successful capture of a phylogenetic estimate for taxa at the University of California Merced Vernal Pools and Grassland Reserve.

Conclusions:

  • The 'opentree' package significantly enhances the accessibility and usability of the Open Tree of Life.
  • These tools empower researchers to conduct complex phylogenetic analyses more efficiently.
  • The project promotes open science principles in evolutionary and biodiversity research.