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- Title
OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life.
- Authors
Mctavish, Emily Jane; Sánchez-Reyes, Luna Luisa; Holder, Mark T
- 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.]
- Subjects
MERCED (Calif.); VERNAL pools; UNIVERSITY of California, San Francisco; DATA analysis; PYTHON programming language; PARSIMONIOUS models
- Publication
Systematic Biology, 2021, Vol 70, Issue 6, p1295
- ISSN
1063-5157
- Publication type
Article
- DOI
10.1093/sysbio/syab033