| Group | Description |
|---|---|
| Acd | Acd file utilities |
| Alignment consensus | Merging sequences to make a consensus |
| Alignment differences | Finding differences between sequences |
| Alignment dot plots | Dot plot sequence comparisons |
| Alignment global | Global sequence alignment |
| Alignment local | Local sequence alignment |
| Alignment multiple | Multiple sequence alignment |
| Assembly fragment assembly | DNA sequence assembly |
| 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 2d structure | Nucleic acid secondary structure |
| Nucleic codon usage | Codon usage analysis |
| Nucleic composition | Composition of nucleotide sequences |
| Nucleic CpG islands | CpG island detection and analysis |
| Nucleic gene finding | Predictions of genes and other genomic features |
| Nucleic motifs | Nucleic acid motif searches |
| Nucleic mutation | Nucleic acid sequence mutation |
| Nucleic primers | Primer prediction |
| Nucleic profiles | Nucleic acid profile generation and searching |
| Nucleic repeats | Nucleic acid repeat detection |
| Nucleic restriction | Restriction enzyme sites in nucleotide sequences |
| Nucleic RNA folding | RNA folding methods and analysis |
| Nucleic transcription | Transcription factors, promoters and terminator prediction |
| Nucleic translation | Translation of nucleotide sequence to protein sequence |
| Phylogeny consensus | Phylogenetic consensus methods |
| Phylogeny continuous characters | Phylogenetic continuous character methods |
| Phylogeny discrete characters | Phylogenetic discrete character methods |
| Phylogeny distance matrix | Phylogenetic distance matrix methods |
| Phylogeny gene frequencies | Phylogenetic gene frequency methods |
| Phylogeny molecular sequence | Phylogenetic tree drawing methods |
| Phylogeny tree drawing | Phylogenetic molecular sequence methods |
| Protein 2d structure | Protein secondary structure |
| Protein 3d structure | Protein tertiary structure |
| Protein composition | Composition of protein sequences |
| Protein motifs | Protein motif searches |
| Protein mutation | Protein sequence mutation |
| Protein profiles | Protein profile generation and searching |
| Test | Testing tools, not for general use. |
| Utils database creation | Database installation |
| Utils database indexing | Database indexing |
| Utils misc | Utility tools |