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| DECIPHER-package | Database Enabled Code for Ideal Probe Hybridization Employing R |
| 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 | Database Enabled Code for Ideal Probe Hybridization Employing R |
| deltaGrules | Free Energy of Hybridization of Probe/Target Quadruplets |
| 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 |
| IdentifyByRank | Identify By Taxonomic Rank |
| IdLengths | Determine the Number of Bases, Nonbases, and Width of Each Sequence |
| MaskAlignment | Masks Highly Variable Regions of An Alignment |
| MODELS | Available Models of DNA Evolution |
| 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. |