Phenex can annotate character matrix file, it 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.

Installation on Windows
On Windows you must be sure to extract the Phenex folder from the zip archive - Phenex will not function properly if run from within the zip archive. Right-click on the downloaded zip file and choose "Extract All...". Use the Extraction Wizard to copy Phenex to a folder on your desktop. You can then move the Phenex folder anywhere you like. Within the Phenex folder, double-click the file Phenex.bat to launch the application.

Running Phenex
After launching Phenex, Java can sometimes be a little slow to start up. If you're running Java 6 or later, you should see a splash screen image shortly after launching. This is followed by a panel informing you that Phenex is checking for ontology updates. If you have not run Phenex before, your computer needs to be online in order for Phenex to download the required ontologies. If you have run Phenex before, Phenex will check for the availability of a newer version of each ontology and download it if necessary. It is okay to work offline if Phenex has previously had a chance to download the ontologies. Phenex performs a check for ontology updates each time it is launched.

Requirements:
* Java

The license of this software is Free, you can free download and free use this graphing software.