Add2DB                  Add Data To A Database
AlignProfiles           Aligns Two Sets of Aligned Sequences
AlignSeqs               Aligns A Set of Unaligned Sequences
Array2Matrix            Creates a Matrix Representation of a Microarray
BrowseDB                View A Database Table In A Web Browser
BrowseSequences         View Sequences In A Web Browser
CalculateEfficiencyArray
                        Predicts the Hybridization Efficiency of
                        Probe/Target Sequence Pairs
CalculateEfficiencyFISH
                        Predicts Thermodynamic Parameters of
                        Probe/Target Sequence Pairs
CalculateEfficiencyPCR
                        Predicts Amplification Efficiency of Primer
                        Sequences
ConsensusSequence       Create A Consensus Sequence
CreateChimeras          Creates Artificial Chimeras
DB2FASTA                Export Database Sequences to FASTA File
DECIPHER-package        Database Enabled Code for Ideal Probe
                        Hybridization Employing R
DesignArray             Designs a set of DNA Microarray Probes for
                        Detecting Sequences
DesignPrimers           Designs PCR Primers Targeting a Specific Group
                        of Sequences
DesignProbes            Designs FISH Probes Targeting a Specific Group
                        of Sequences
DistanceMatrix          Calculate the Distance Between DNA Sequences
FindChimeras            Find Chimeras In A Sequence Database
FormGroups              Forms Groups By Rank
IdClusters              Cluster Sequences By Distance
IdConsensus             Create Consensus Sequences by Groups
IdLengths               Determine the Number of Bases, Nonbases, and
                        Width of Each Sequence
IdentifyByRank          Identify By Taxonomic Rank
MODELS                  Available Models of DNA Evolution
MaskAlignment           Masks Highly Variable Regions of An Alignment
NNLS                    Sequential Coordinate-wise Algorithm for the
                        Non-negative Least Squares Problem
SearchDB                Obtain Specific Sequences from A Database
Seqs2DB                 Add Sequences from Text File to Database
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
