An R package for analysing ontologies and protein domain annotations has been published in PLoS Computational Biology (http://dx.doi.org/10.1371/journal.pcbi.1003929. The package is distributed as part of CRAN (http://cran.r-project.org/package=dcGOR, and also at GitHub for version control.
The dedicated website is available in http://supfam.org/dcGOR, from which several demos are also provided:
1. Analysing SCOP domains: http://supfam.org/dcGOR/demo-Fang.html
2. Analysing Pfam domains: http://supfam.org/dcGOR/demo-Basu.html
3. Analysing InterPro domains: http://supfam.org/dcGOR/demo-Customisation.html
