| Alignments | embaln | Sequence alignment |
| Comments | embcom | Complexity |
| Consensus sequences | embcons | Consensus |
| Data file utilities | embdata | Data files |
| Database indexing using EMBL-CD indices | embdbi | Database index |
| Domainatrix package algorithms | embdmx | Domainatrix methods |
| Domain algorithms | embdomain | Domain methods |
| EST algorithms | embest | EST methods |
| Exit calls for applications | embexit | Exit methods |
| Groups of applications | embgroup | Groups |
| Isoelectric point utilities | embiep | Protein properties |
| Indexing databases using B+ trees | embindex | Indexing |
| Initialising internals | embinit | Initialization |
| Comparison matrices | embmat | Comparison matrices |
| Miscellaneous methods | embmisc | Miscellaneous methods |
| Molecular fragment algorithms | embmol | Molecular fragments |
| N-mer (word) algorithms | embnmer | Word (n-mer) methods |
| Pattern matching algorithms | embpat | Pattern matching methods |
| Pattern list file reading | embpatlist | Pattern list input methods |
| Protein databank (PDB) structure file utilities | embpdb | Protein data bank |
| Properties of protein sequences | embprop | Sequence properties |
| Reading data files | embread | Reading data files |
| Showing sequences in pretty formats | embshow | Show (display) methods |
| Signatures of protein domains | embsig | Signature methods |
| Word matching algorithms | embword | Word methods |
| Include file for all applications | emboss | Master include file |