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| DECIPHER-package | Tools for curating, analyzing, and manipulating biological sequences |
| 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 |
| c.Taxa | Taxa training and testing objects |
| 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 |
| CorrectFrameshifts | Corrects Frameshift Errors In Protein Coding Sequences |
| CreateChimeras | Create Artificial Chimeras |
| DB2Seqs | Export Database Sequences to a FASTA or FASTQ File |
| DECIPHER | Tools for curating, analyzing, and manipulating biological 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 |
| 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 |
| FindSynteny | Finds Synteny in a Sequence Database |
| FormGroups | Forms Groups By Rank |
| HEC_MI1 | Mutual Information for Protein Secondary Structure Prediction |
| HEC_MI2 | Mutual Information for Protein Secondary Structure Prediction |
| IdClusters | Cluster Sequences By Distance or Sequence |
| IdConsensus | Create Consensus Sequences by Groups |
| IdentifyByRank | Identify By Taxonomic Rank |
| IdLengths | Determine the Number of Bases, Nonbases, and Width of Each Sequence |
| IdTaxa | Assign Sequences a Taxonomic Classification |
| LearnTaxa | Train a Classifier for Assigning Taxonomy |
| MaskAlignment | Mask Highly Variable Regions of An Alignment |
| MeltDNA | Simulate Melting of DNA |
| MIQS | MIQS Amino Acid Substitution Matrix |
| MODELS | Available Models of DNA Evolution |
| NNLS | Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem |
| OrientNucleotides | Orient Nucleotide Sequences |
| pairs.Synteny | Synteny blocks and hits |
| PFASUM | PFASUM Amino Acid Substitution Matrices |
| plot.Synteny | Synteny blocks and hits |
| plot.Taxa | Taxa training and testing objects |
| PredictDBN | Predict RNA Secondary Structure in Dot-Bracket Notation |
| PredictHEC | Predict Protein Secondary Structure as Helix, Beta-Sheet, or Coil |
| print.Synteny | Synteny blocks and hits |
| print.Taxa | Taxa training and testing objects |
| ReadDendrogram | Read a Dendrogram from a Newick Formatted File |
| RemoveGaps | Remove Gap Characters in Sequences |
| 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 |
| 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 |
| TrimDNA | Trims DNA Sequences to the High Quality Region Between Patterns |
| WriteDendrogram | Write a Dendrogram to Newick Format |
| [.Synteny | Synteny blocks and hits |
| [.Taxa | Taxa training and testing objects |