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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
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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.
Systematic Biology
|May 10, 2021
Summary
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.
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.
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