ArticlebioRxiv : the preprint server for biology2023
PhyloMatcher: a tool for resolving conflicts in taxonomic nomenclature.
Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Summary: Large-scale comparative studies rely on the application of both phylogenetic trees and phenotypic data, both of which come from a variety of sources, but due to the changing nature of phylogenetic classification over time, many taxon names in comparative datasets do not match the nomenclature in phylogenetic trees. Manual curation of taxonomic synonyms in large comparative datasets can be daunting. To address this issue, we introduce PhyloMatcher, a tool which allows for programmatic querying of two commonly used taxonomic databases to find associated synonyms with given target species names. Availability and implementation: PhyloMatcher is easily installed as a Python package with pip, or as a standalone GUI application. PhyloMatcher source code and documentation are freely available at https://github.com/Lswhiteh/PhyloMatcher, the GUI application can be downloaded from the Releases page. Contact: Lswhiteh@unc.edu. Supplemental Information: We provide documentation for PhyloMatcher, including walkthrough instructions for the GUI application on the Releases page of https://github.com/Lswhiteh/PhyloMatcher.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.