Man pages for DECIPHER
Tools for curating, analyzing, and manipulating biological sequences

AA_REDUCEDReduced amino acid alphabets
Add2DBAdd Data to a Database
AdjustAlignmentImprove An Existing Alignment By Adjusting Gap Placements
AlignDBAlign Two Sets of Aligned Sequences in a Sequence Database
AlignProfilesAlign Two Sets of Aligned Sequences
AlignSeqsAlign a Set of Unaligned Sequences
AlignSyntenyPairwise Aligns Syntenic Blocks
AlignTranslationAlign Sequences By Their Amino Acid Translation
AmplifyDNASimulate Amplification of DNA by PCR
Array2MatrixCreate a Matrix Representation of a Microarray
BrowseDBView a Database Table in a Web Browser
BrowseSeqsView Sequences in a Web Browser
CalculateEfficiencyArrayPredict the Hybridization Efficiency of Probe/Target Sequence...
CalculateEfficiencyFISHPredict Thermodynamic Parameters of Probe/Target Sequence...
CalculateEfficiencyPCRPredict Amplification Efficiency of Primer Sequences
CodecCompression/Decompression of Character Vectors
ConsensusSequenceCreate a Consensus Sequence
CorrectFrameshiftsCorrects Frameshift Errors In Protein Coding Sequences
CreateChimerasCreate Artificial Chimeras
DB2SeqsExport Database Sequences to a FASTA or FASTQ File
DECIPHER-packageTools for curating, analyzing, and manipulating biological...
deltaGrulesFree Energy of Hybridization of Probe/Target Quadruplets on...
deltaHrulesChange in Enthalpy of Hybridization of Primer/Target...
deltaSrulesChange in Entropy of Hybridization of Primer/Target...
DesignArrayDesign a Set of DNA Microarray Probes for Detecting Sequences
DesignPrimersDesign PCR Primers Targeting a Specific Group of Sequences
DesignProbesDesign FISH Probes Targeting a Specific Group of Sequences
DesignSignaturesDesign PCR Primers for Amplifying Group-Specific Signatures
DigestDNASimulate Restriction Digestion of DNA
DisambiguateExpand Ambiguities into All Permutations of a DNAStringSet
DistanceMatrixCalculate the Distances Between Sequences
FindChimerasFind Chimeras in a Sequence Database
FindSyntenyFinds Synteny in a Sequence Database
FormGroupsForms Groups By Rank
HEC_MIMutual Information for Protein Secondary Structure Prediction
IdClustersCluster Sequences By Distance or Sequence
IdConsensusCreate Consensus Sequences by Groups
IdentifyByRankIdentify By Taxonomic Rank
IdLengthsDetermine the Number of Bases, Nonbases, and Width of Each...
IdTaxaAssign Sequences a Taxonomic Classification
LearnTaxaTrain a Classifier for Assigning Taxonomy
MaskAlignmentMask Highly Variable Regions of An Alignment
MeltDNASimulate Melting of DNA
MIQSMIQS Amino Acid Substitution Matrix
MODELSAvailable Models of DNA Evolution
NNLSSequential Coordinate-wise Algorithm for the Non-negative...
OrientNucleotidesOrient Nucleotide Sequences
PFASUMPFASUM Amino Acid Substitution Matrices
PredictDBNPredict RNA Secondary Structure in Dot-Bracket Notation
PredictHECPredict Protein Secondary Structure as Helix, Beta-Sheet, or...
ReadDendrogramRead a Dendrogram from a Newick Formatted File
RemoveGapsRemove Gap Characters in Sequences
RESTRICTION_ENZYMESCommon Restriction Enzyme's Cut Sites
SearchDBObtain Specific Sequences from a Database
Seqs2DBAdd Sequences from Text File to Database
StaggerAlignmentProduce a Staggered Alignment
Synteny-classSynteny blocks and hits
Taxa-classTaxa training and testing objects
TerminalCharDetermine the Number of Terminal Characters
TileSeqsForm a Set of Tiles for Each Group of Sequences.
TrainingSet_16STraining Set for Classification of 16S rRNA Gene Sequences
TrimDNATrims DNA Sequences to the High Quality Region Between...
WriteDendrogramWrite a Dendrogram to Newick Format
DECIPHER documentation built on Feb. 8, 2019, 6 p.m.