DECIPHER-package	DECIPHER-package
AA_REDUCED	AA_REDUCED
Add2DB	Add2DB
AdjustAlignment	AdjustAlignment
AlignDB	AlignDB
AlignProfiles	AlignProfiles
AlignSeqs	AlignSeqs
AlignSynteny	AlignSynteny
AlignTranslation	AlignTranslation
AmplifyDNA	AmplifyDNA
Array2Matrix	Array2Matrix
BrowseDB	BrowseDB
BrowseSeqs	BrowseSeqs
c.Taxa	Taxa-class
CalculateEfficiencyArray	CalculateEfficiencyArray
CalculateEfficiencyFISH	CalculateEfficiencyFISH
CalculateEfficiencyPCR	CalculateEfficiencyPCR
Codec	Codec
ConsensusSequence	ConsensusSequence
CorrectFrameshifts	CorrectFrameshifts
CreateChimeras	CreateChimeras
DB2Seqs	DB2Seqs
DECIPHER	DECIPHER-package
deltaGrules	deltaGrules
deltaHrules	deltaHrules
deltaSrules	deltaSrules
DesignArray	DesignArray
DesignPrimers	DesignPrimers
DesignProbes	DesignProbes
DesignSignatures	DesignSignatures
DigestDNA	DigestDNA
Disambiguate	Disambiguate
DistanceMatrix	DistanceMatrix
FindChimeras	FindChimeras
FindSynteny	FindSynteny
FormGroups	FormGroups
HEC_MI1	HEC_MI
HEC_MI2	HEC_MI
IdClusters	IdClusters
IdConsensus	IdConsensus
IdentifyByRank	IdentifyByRank
IdLengths	IdLengths
IdTaxa	IdTaxa
LearnTaxa	LearnTaxa
MaskAlignment	MaskAlignment
MeltDNA	MeltDNA
MIQS	MIQS
MODELS	MODELS
NNLS	NNLS
OrientNucleotides	OrientNucleotides
pairs.Synteny	Synteny-class
PFASUM	PFASUM
plot.Synteny	Synteny-class
plot.Taxa	Taxa-class
PredictDBN	PredictDBN
PredictHEC	PredictHEC
print.Synteny	Synteny-class
print.Taxa	Taxa-class
ReadDendrogram	ReadDendrogram
RemoveGaps	RemoveGaps
RESTRICTION_ENZYMES	RESTRICTION_ENZYMES
SearchDB	SearchDB
Seqs2DB	Seqs2DB
StaggerAlignment	StaggerAlignment
Synteny-class	Synteny-class
Taxa-class	Taxa-class
TerminalChar	TerminalChar
TileSeqs	TileSeqs
TrainingSet_16S	TrainingSet_16S
TrimDNA	TrimDNA
WriteDendrogram	WriteDendrogram
[.Synteny	Synteny-class
[.Taxa	Taxa-class
