Pellet is an open-source Java based OWL DL reasoner. It can be used in conjunction with either Jena or OWL API libraries. Pellet provides functionalities to check the consistency of ontologies, classify the taxonomy, check entailments, give explanations, and answer SPARQL-DL queries.
Pellet comes with a simple command line interface to demonstrate some of its capabilities. This program provides options to check the consistency of an ontology, find unsatisfiable concepts, display the class hierarchy (with instances if desired), answer a SPARQL-DL query.
To run the command line version simply execute the following command
pellet.sh help
Running this command will print the options available.
You can access Pellet from Java applications using one of two different APIs designed to support Jena and OWL API libraries. The functionality in both packages is almost equivalent. See the javadocs for the details of interfaces and check out the examples directory for sample code. You can find the answers to some Frequently Asked Questions in Pellet FAQ.
If you are interested in a GUI, you can use SWOOP which uses Pellet for reasoning.
There is a mailing list for questions and feedback: pellet-users@lists.owldl.com. You can subscribe to the list and see the archives here: http://lists.owldl.com/mailman/listinfo/pellet-users.