Phenex for Linux builds on Phenote and OBO edit from the OBO project. Phenex for Linux is an application for annotating character matrix files with ontology terms. Its 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 for Linux saves ontology annotations alongside traditional character matrix data using the new NeXML format standard for evolutionary data.