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Phenex is an application for annotating character matrix files with ontology terms. Character states can be annotated using the Entity-Quality syntax for ontologically describing phenotypes. In addition, taxon entries can be annotated with identifiers from a taxonomy ontology. Phenex saves ontology annotations alongside traditional character matrix data using the new NeXML format standard for evolutionary data. Phenex builds on Phenote and OBO-Edit from the OBO project. Jim Balhoff is the lead developer of Phenex.