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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. It has two main goals. The primary one is to facilitate automated testing that the semantics of the logical definitions imply (“resolve to”) the correct nodes in the reference tree as clade ancestors. 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). When run as part of an automated testing workflow, JPhyloRef reports test results in the cross-platform Test Anything Protocol (TAP) format. When used to find clade ancestor nodes implied by logical clade definitions, results are returned as a JSON object. JPhyloRef uses the OWL API reference library for reading Web Ontology Language (OWL) ontologies, and for the actual ontology reasoning step it uses an external and configurable OWL reasoner.