AA_REDUCED              Reduced amino acid alphabets
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
AlignSynteny            Pairwise Aligns Syntenic Blocks
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
Codec                   Compression/Decompression of Character Vectors
ConsensusSequence       Create a Consensus Sequence
Cophenetic              Compute cophenetic distances on dendrogram
                        objects
CorrectFrameshifts      Corrects Frameshift Errors In Protein Coding
                        Sequences
CreateChimeras          Create Artificial Chimeras
DB2Seqs                 Export Database Sequences to a FASTA or FASTQ
                        File
DECIPHER-package        Tools for curating, analyzing, and manipulating
                        biological sequences
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
DetectRepeats           Detect Repeats in a Sequence
DigestDNA               Simulate Restriction Digestion of DNA
Disambiguate            Expand Ambiguities into All Permutations of a
                        DNAStringSet
DistanceMatrix          Calculate the Distances Between Sequences
ExtractGenes            Extract Predicted Genes from a Genome
FindChimeras            Find Chimeras in a Sequence Database
FindGenes               Find Genes in a Genome
FindNonCoding           Find Non-Coding RNAs in a Genome
FindSynteny             Finds Synteny in a Sequence Database
FormGroups              Forms Groups By Rank
Genes-class             Genes objects and accessors
HEC_MI1                 Mutual Information for Protein Secondary
                        Structure Prediction
IdClusters              Cluster Sequences By Similarity
IdConsensus             Create Consensus Sequences by Groups
IdLengths               Determine the Number of Bases, Nonbases, and
                        Width of Each Sequence
IdTaxa                  Assign Sequences a Taxonomic Classification
IdentifyByRank          Identify By Taxonomic Rank
LearnNonCoding          Learn a Non-Coding RNA Model
LearnTaxa               Train a Classifier for Assigning Taxonomy
MIQS                    MIQS Amino Acid Substitution Matrix
MODELS                  Available Models of Sequence Evolution
MapCharacters           Map Changes in Ancestral Character States
MaskAlignment           Mask Highly Variable Regions of An Alignment
MeltDNA                 Simulate Melting of DNA
NNLS                    Sequential Coordinate-wise Algorithm for the
                        Non-negative Least Squares Problem
NonCoding-class         NonCoding Objects and Methods
NonCodingRNA_Archaea    NonCoding Models for Common Non-Coding RNA
                        Families
OrientNucleotides       Orient Nucleotide Sequences
PFASUM                  PFASUM Amino Acid Substitution Matrices
PredictDBN              Predict RNA Secondary Structure in Dot-Bracket
                        Notation
PredictHEC              Predict Protein Secondary Structure as Helix,
                        Beta-Sheet, or Coil
RESTRICTION_ENZYMES     Common Restriction Enzyme's Cut Sites
ReadDendrogram          Read a Dendrogram from a Newick Formatted File
RemoveGaps              Remove Gap Characters in Sequences
ScoreAlignment          Score a Multiple Sequence Alignment
SearchDB                Obtain Specific Sequences from a Database
Seqs2DB                 Add Sequences from Text File to Database
StaggerAlignment        Produce a Staggered Alignment
Synteny-class           Synteny blocks and hits
Taxa-class              Taxa training and testing objects
TerminalChar            Determine the Number of Terminal Characters
TileSeqs                Form a Set of Tiles for Each Group of
                        Sequences.
TrainingSet_16S         Training Set for Classification of 16S rRNA
                        Gene Sequences
TreeLine                Construct a Phylogenetic Tree
TrimDNA                 Trims DNA Sequences to the High Quality Region
                        Between Patterns
WriteDendrogram         Write a Dendrogram to Newick Format
WriteGenes              Write Genes to a File
deltaGrules             Free Energy of Hybridization of Probe/Target
                        Quadruplets on Microarrays
deltaHrules             Change in Enthalpy of Hybridization of DNA/DNA
                        Quadruplets in Solution
deltaHrulesRNA          Change in Enthalpy of Hybridization of RNA/RNA
                        Quadruplets in Solution
deltaSrules             Change in Entropy of Hybridization of DNA/DNA
                        Quadruplets in Solution
deltaSrulesRNA          Change in Entropy of Hybridization of RNA/RNA
                        Quadruplets in Solution
