An R package for analysing ontologies and protein domain annotations has been published in PLoS Computational Biology. The package is distributed as part of CRAN, and also at GitHub for version control.

The dedicated website is available in http://supfam.org/dcGOR, from which demos are also provided:

1. Analysing SCOP domains
2. Analysing Pfam domains
3. Analysing InterPro domains
4. Creating domain-centric ontology and its usage for computational prediction and evaluation

Newly added functionalities are:

1. to create domain-centric ontologies
2. to predict and assess ontology terms for input protein sequences, precisely domain content in the form of architectures
3. to reconstruct ancestral discrete characters using maximum likelihood/parsimony.