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DECIPHER (version 2.0.2)
Tools for curating, analyzing, and manipulating biological sequences
Description
A toolset for deciphering and managing biological sequences.
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Version
Version
2.0.2
1.16.0
1.14.5
1.12.0
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Version
2.0.2
License
GPL-3
Maintainer
Erik Wright
Last Published
June 7th, 2016
Functions in DECIPHER (2.0.2)
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CalculateEfficiencyPCR
Predict Amplification Efficiency of Primer Sequences
AdjustAlignment
Improve An Existing Alignment By Adjusting Gap Placements
MaskAlignment
Mask Highly Variable Regions of An Alignment
AlignSeqs
Align a Set of Unaligned Sequences
DesignSignatures
Design PCR Primers for Amplifying Group-Specific Signatures
DistanceMatrix
Calculate the Distances Between Sequences
SearchDB
Obtain Specific Sequences from a Database
IdConsensus
Create Consensus Sequences by Groups
WriteDendrogram
Write a Dendrogram to Newick Format
TileSeqs
Form a Set of Tiles for Each Group of Sequences.
Seqs2DB
Add Sequences from Text File to Database
AlignProfiles
Align Two Sets of Aligned Sequences
BrowseSeqs
View Sequences in a Web Browser
CalculateEfficiencyFISH
Predict Thermodynamic Parameters of Probe/Target Sequence Pairs
Array2Matrix
Create a Matrix Representation of a Microarray
DesignPrimers
Design PCR Primers Targeting a Specific Group of Sequences
DB2Seqs
Export Database Sequences to a FASTA or FASTQ File
MIQS
MIQS Amino Acid Substitution Matrix
CalculateEfficiencyArray
Predict the Hybridization Efficiency of Probe/Target Sequence Pairs
BrowseDB
View a Database Table in a Web Browser
DesignProbes
Design FISH Probes Targeting a Specific Group of Sequences
FormGroups
Forms Groups By Rank
IdentifyByRank
Identify By Taxonomic Rank
DECIPHER-package
Tools for curating, analyzing, and manipulating biological sequences
MODELS
Available Models of DNA Evolution
AlignDB
Align Two Sets of Aligned Sequences in a Sequence Database
OrientNucleotides
Orient nucleotide sequences
MeltDNA
Simulate Melting of DNA
deltaGrules
Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays
deltaHrules
Change in Enthalpy of Hybridization of Primer/Target Quadruplets in Solution
CreateChimeras
Create Artificial Chimeras
CorrectFrameshifts
Corrects Frameshift Errors In Protein Coding Sequences
AlignSynteny
Pairwise Aligns Syntenic Blocks
AlignTranslation
Align Sequences By Their Amino Acid Translation
Codec
Compression/Decompression of Character Vectors
IdLengths
Determine the Number of Bases, Nonbases, and Width of Each Sequence
Disambiguate
Expand Ambiguities into All Permutations of a DNAStringSet
FindChimeras
Find Chimeras in a Sequence Database
HEC_MI
Mutual Information for Protein Secondary Structure Prediction
RESTRICTION_ENZYMES
Common Restriction Enzyme's Cut Sites
DigestDNA
Simulate Restriction Digestion of DNA
Add2DB
Add Data to a Database
AmplifyDNA
Simulate Amplification of DNA by PCR
deltaSrules
Change in Entropy of Hybridization of Primer/Target Quadruplets in Solution
ReadDendrogram
Read a Dendrogram from a Newick Formatted File
NNLS
Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem
Synteny
Synteny blocks and hits
ConsensusSequence
Create a Consensus Sequence
DesignArray
Design a set of DNA Microarray Probes for Detecting Sequences
TerminalChar
Determine the Number of Terminal Characters
StaggerAlignment
Produce a Staggered Alignment
FindSynteny
Finds Synteny in a Sequence Database
IdClusters
Cluster Sequences By Distance or Sequence
PredictHEC
Predict Protein Secondary Structure