Application Groups

Group	Description
Acd	Acd file utilities
Alignment	Sequence comparison and alignment
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
Data resources	Data resources
Data retrieval	Data retrieval
Data retrieval chemistry data	Chemistry data retrieval
Data retrieval feature data	Sequence feature data retrieval
Data retrieval ontology data	Ontology data retrieval
Data retrieval resource data	Resource data retrieval
Data retrieval sequence data	Sequence data retrieval
Data retrieval sequence data assembly data	Sequence assembly data retrieval
Data retrieval text data	Text data retrieval
Data retrieval tool data	Tool data retrieval
Data retrieval url data	Url data retrieval
Display	Publication-quality display
Documentation	Documentation
Edit	Data file and content editing
Enzyme kinetics	Enzyme kinetics calculations
Feature tables	Manipulation and display of sequence annotation
HMM	Hidden markov model analysis
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 functional sites	Nucleic acid functional sites
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 properties	Nucleic acid physicochemical properties
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
Ontology	Ontologies
Ontology edam	Edam ontology
Ontology go	Go gene ontology
Ontology taxonomy	Ncbi taxonomy
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 molecular sequence methods
Phylogeny tree drawing	Phylogenetic tree drawing methods
Protein 2d structure	Protein secondary structure
Protein 3d structure	Protein tertiary structure
Protein composition	Composition of protein sequences
Protein domains	Protein domain analysis
Protein functional sites	Protein functional sites
Protein modifications	Protein post-translational modifications
Protein motifs	Protein motif searches
Protein mutation	Protein sequence mutation
Protein profiles	Protein profile generation and searching
Protein properties	Protein physicochemical properties
Test	Testing tools, not for general use.
Utils	Utility tools
Utils database creation	Database installation
Utils database indexing	Database indexing