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

Abstract The Open Tree of Life project constructs a comprehensive, dynamic, and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified...

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Published inSystematic biology Vol. 70; no. 6; pp. 1295 - 1301
Main Authors Mctavish, Emily Jane, Sánchez-Reyes, Luna Luisa, Holder, Mark T
Format Journal Article
LanguageEnglish
Published England Oxford University Press 13.10.2021
Subjects
Data Analysis
Humans
Phylogeny
Software
Software for Systematics and Evolution
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Summary:Abstract The Open Tree of Life project constructs a comprehensive, dynamic, and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the Python package opentree, which provides a user friendly Python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.[Evolution; open science; phylogenetics; Python; taxonomy.]
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ISSN:1063-5157
1076-836X
1076-836X
DOI:10.1093/sysbio/syab033