| Program name | Description | 
|---|
| psiphi | Phi and psi torsion angles from protein coordinates | 
| domainreso | Remove low resolution domains from a DCF file | 
| domainalign | Generate alignments (DAF file) for nodes in a DCF file | 
| domainrep | Reorder DCF file to identify representative structures | 
| seqalign | Extend alignments (DAF file) with sequences (DHF file) | 
| seqfraggle | Removes fragment sequences from DHF files | 
| seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file | 
| seqsort | Remove ambiguous classified sequences from DHF files | 
| seqwords | Generates DHF files from keyword search of UniProt | 
| libgen | Generate discriminating elements from alignments | 
| matgen3d | Generate a 3D-1D scoring matrix from CCF files | 
| rocon | Generates a hits file from comparing two DHF files | 
| rocplot | Performs ROC analysis on hits files | 
| siggen | Generates a sparse protein signature from an alignment | 
| siggenlig | Generate ligand-binding signatures from a CON file | 
| sigscan | Generate hits (DHF file) from a signature search | 
| sigscanlig | Search ligand-signature library & write hits (LHF file) | 
| contacts | Generate intra-chain CON files from CCF files | 
| interface | Generate inter-chain CON files from CCF files |