Add2DB                  Add Data To A Database
AdjustAlignment         Improve An Existing Alignment By Adjusting Gap
                        Placements
AlignDB                 Align Two Sets of Aligned Sequences In A
                        Sequence Database
AlignProfiles           Align Two Sets of Aligned Sequences
AlignSeqs               Align A Set of Unaligned Sequences
AlignTranslation        Align Sequences By Their Amino Acid Translation
AmplifyDNA              Simulate Amplification of DNA by PCR
Array2Matrix            Create a Matrix Representation of a Microarray
BrowseDB                View A Database Table In A Web Browser
BrowseSeqs              View Sequences In A Web Browser
CalculateEfficiencyArray
                        Predict the Hybridization Efficiency of
                        Probe/Target Sequence Pairs
CalculateEfficiencyFISH
                        Predict Thermodynamic Parameters of
                        Probe/Target Sequence Pairs
CalculateEfficiencyPCR
                        Predict Amplification Efficiency of Primer
                        Sequences
ConsensusSequence       Create A Consensus Sequence
CreateChimeras          Create Artificial Chimeras
DB2Seqs                 Export Database Sequences to a FASTA or FASTQ
                        File
DECIPHER-deprecated     Deprecated functions in package 'DECIPHER'
DECIPHER-package        Database Enabled Code for Ideal Probe
                        Hybridization Employing R
DesignArray             Design a set of DNA Microarray Probes for
                        Detecting Sequences
DesignPrimers           Design PCR Primers Targeting a Specific Group
                        of Sequences
DesignProbes            Design FISH Probes Targeting a Specific Group
                        of Sequences
DesignSignatures        Design PCR Primers for Amplifying
                        Group-Specific Signatures
DigestDNA               Simulate Restriction Digestion of DNA
Disambiguate            Expand Ambiguities into All Permutations of a
                        DNAStringSet
DistanceMatrix          Calculate the Distances Between Sequences
FindChimeras            Find Chimeras In A Sequence Database
FormGroups              Forms Groups By Rank
HEC_MI1                 Mutual Information for Protein Secondary
                        Structure Prediction
IdClusters              Cluster Sequences By Distance or Sequence
IdConsensus             Create Consensus Sequences by Groups
IdLengths               Determine the Number of Bases, Nonbases, and
                        Width of Each Sequence
IdentifyByRank          Identify By Taxonomic Rank
MIQS                    MIQS Amino Acid Substitution Matrix
MODELS                  Available Models of DNA Evolution
MaskAlignment           Masks Highly Variable Regions of An Alignment
MeltDNA                 Simulate Melting of DNA
NNLS                    Sequential Coordinate-wise Algorithm for the
                        Non-negative Least Squares Problem
PredictHEC              Predict Protein Secondary Structure
RESTRICTION_ENZYMES     Common Restriction Enzyme's Cut Sites
SearchDB                Obtain Specific Sequences from A Database
Seqs2DB                 Add Sequences from Text File to Database
StaggerAlignment        Produce a Staggered Alignment
TerminalChar            Determine the Number of Terminal Characters
TileSeqs                Form a Set of Tiles for Each Group of
                        Sequences.
deltaGrules             Free Energy of Hybridization of Probe/Target
                        Quadruplets on Microarrays
deltaHrules             Change in Enthalpy of Hybridization of
                        Primer/Target Quadruplets in Solution
deltaSrules             Change in Entropy of Hybridization of
                        Primer/Target Quadruplets in Solution
