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• contacts - Generate intra-chain CON files from CCF files (part of the EMBOSS package)
• interface - Generate inter-chain CON files from CCF files (part of the EMBOSS package)
• Psipred - Predict protein structure
• seqalign - Extend alignments (DAF file) with sequences (DHF file) (part of the EMBOSS package)
• seqsearch - Generate PSI-BLAST hits (DHF file) from a DAF file (part of the EMBOSS package)
• seqsort - Remove ambiguously classified sequences from DHF files (part of the EMBOSS package)
• seqwords - Generate DHF files from a keyword search of UniProt (part of the EMBOSS package)
• siggen - Generate a sparse protein signature from an alignment (part of the EMBOSS package)
• sigscan - Generate hits (DHF file) from a signature search (part of the EMBOSS package)