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JPhyloRef is a command line tool as well as a web service for reasoning with ontologies containing logical definitions of clades, called phyloreferences, and their accompanying reference phylogenetic trees ... The secondary goal is to enable integration with external tools that need to obtain the clade ancestor node(s) resulting from a given ontology of phyloreferences and reference tree(s). ... Acknowledgements This work was funded by the US National Science Foundation through collaborative grants DBI-1458484 and DBI-1458604 to Hilmar Lapp (Duke University) and Nico Cellinese (University of Florida ...doi:10.21105/joss.03374 fatcat:llqpdarhwrefpg53z4lv52z4qq
To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software ... Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades. ... ACKNOWLEDGEMENTS We thank Daniel Caetano and an anonymous reviewer for helping to improve this manuscript through their thoughtful and constructive comments. ADDITIONAL INFORMATION AND DECLARATIONS ...doi:10.7717/peerj.12618 pmid:35186448 pmcid:PMC8855714 fatcat:f7lz6zznvjevhoubjcqnmmz55a