|   | Application Groups | 
| 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 | 
| 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 |