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bioRxiv · 10.1101/2020.09.15.299156

Physcraper: A Python package for continual update of evolutionary estimates using the Open Tree of Life

Sanchez Reyes, L. L.·Kandziora, M.·McTavish, E. J.
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Abstract

O_LIPhylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and nonspecialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. C_LIO_LIPhyscraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. C_LIO_LIPhyscraper can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). C_LIO_LIThe Physcraper workflow demonstrates the benefits of doing open science for phylogenetics, encour-aging researchers to strive for better sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and use are available at https://physcraper.readthedocs. C_LI

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Sanchez Reyes, L. L., Kandziora, M., McTavish, E. J.. 2020-09-17. Physcraper: A Python package for continual update of evolutionary estimates using the Open Tree of Life. https://doi.org/10.1101/2020.09.15.299156

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