| Acd | ACD file utilities |
| Alignment |
| Alignment:Consensus | Merging sequences to make a consensus |
| Consensus | Merging sequences to make a consensus |
| Differences | Finding differences between sequences |
| Dot_plots | Dot plot sequence comparisons |
| Global | Global sequence alignment |
| Local | Local sequence alignment |
| Multiple | Multiple sequence alignment |
| Display | Publication-quality display |
| Edit | Sequence editing |
| Enzyme_Kinetics | Enzyme kinetics calculations |
| Feature_tables | Manipulation and display of sequence annotation |
| HMM | Hidden Markov Model analysis |
| Information | Information and general help for users |
| Menus | Menu interface(s) |
| Nucleic |
| Nucleic:2D_structure | Nucleic acid secondary structure |
| 2D_structure | Nucleic acid secondary structure |
| Codon_usage | Codon usage analysis |
| Composition | Composition of nucleotide sequences |
| CpG_islands | CpG island detection and analysis |
| Gene_finding | Predictions of genes and other genomic features |
| Motifs | Nucleic acid motif searches |
| Mutation | Nucleic acid sequence mutation |
| Profiles | Nucleic acid profile generation and searching |
| Primers | Primer prediction |
| Repeats | Nucleic acid repeat detection |
| RNA_folding | RNA folding methods and analysis |
| Restriction | Restriction enzyme sites in nucleotide sequences |
| Transcription | Transcription factors, promoters and terminator prediction |
| Translation | Translation of nucleotide sequence to protein sequence |
| Phylogeny |
| Phylogeny:Consensus | Phylogenetic consensus methods |
| Consensus | Phylogenetic consensus methods |
| Continuous_characters | Phylogenetic continuous character methods |
| Discrete_characters | Phylogenetic discrete character methods |
| Distance_matrix | Phylogenetic distance matrix methods |
| Gene_frequencies | Phylogenetic gene frequency methods |
| Molecular_sequence | Phylogenetic tree drawing methods |
| Tree_drawing | Phylogenetic molecular sequence methods |
| Protein |
| Protein:2D_structure | Protein secondary structure |
| 2D_structure | Protein secondary structure |
| 3D_structure | Protein tertiary structure |
| Composition | Composition of protein sequences |
| Motifs | Protein motif searches |
| Mutation | Protein sequence mutation |
| Profiles | Protein profile generation and searching |
| Test | Testing tools, not for general use. |
| Utils |
| Utils:Database_creation | Database installation |
| Database_creation | Database installation |
| Database_indexing | Database indexing |
| Misc | Utility tools |