B.2. Application Groups (release R6)

Table B.1. Application Groups (release R6)
AcdACD file utilities
Alignment:ConsensusMerging sequences to make a consensus
ConsensusMerging sequences to make a consensus
DifferencesFinding differences between sequences
Dot_plotsDot plot sequence comparisons
GlobalGlobal sequence alignment
LocalLocal sequence alignment
MultipleMultiple sequence alignment
DisplayPublication-quality display
EditSequence editing
Enzyme_KineticsEnzyme kinetics calculations
Feature_tablesManipulation and display of sequence annotation
HMMHidden Markov Model analysis
InformationInformation and general help for users
MenusMenu interface(s)
Nucleic:2D_structureNucleic acid secondary structure
2D_structureNucleic acid secondary structure
Codon_usageCodon usage analysis
CompositionComposition of nucleotide sequences
CpG_islandsCpG island detection and analysis
Gene_findingPredictions of genes and other genomic features
MotifsNucleic acid motif searches
MutationNucleic acid sequence mutation
ProfilesNucleic acid profile generation and searching
PrimersPrimer prediction
RepeatsNucleic acid repeat detection
RNA_foldingRNA folding methods and analysis
RestrictionRestriction enzyme sites in nucleotide sequences
TranscriptionTranscription factors, promoters and terminator prediction
TranslationTranslation of nucleotide sequence to protein sequence
Phylogeny:ConsensusPhylogenetic consensus methods
ConsensusPhylogenetic consensus methods
Continuous_charactersPhylogenetic continuous character methods
Discrete_charactersPhylogenetic discrete character methods
Distance_matrixPhylogenetic distance matrix methods
Gene_frequenciesPhylogenetic gene frequency methods
Molecular_sequencePhylogenetic tree drawing methods
Tree_drawingPhylogenetic molecular sequence methods
Protein:2D_structureProtein secondary structure
2D_structureProtein secondary structure
3D_structureProtein tertiary structure
CompositionComposition of protein sequences
MotifsProtein motif searches
MutationProtein sequence mutation
ProfilesProtein profile generation and searching
TestTesting tools, not for general use.
Utils:Database_creationDatabase installation
Database_creationDatabase installation
Database_indexingDatabase indexing
MiscUtility tools