DECIPHER-package	DECIPHER-package
AA_REDUCED	AA_REDUCED
Add2DB	Add2DB
AdjustAlignment	AdjustAlignment
AlignDB	AlignDB
AlignPairs	AlignPairs
AlignProfiles	AlignProfiles
AlignSeqs	AlignSeqs
AlignSynteny	AlignSynteny
AlignTranslation	AlignTranslation
AmplifyDNA	AmplifyDNA
Array2Matrix	Array2Matrix
as.dist.Synteny	Synteny-class
BLOSUM	BLOSUM
BrowseDB	BrowseDB
BrowseSeqs	BrowseSeqs
c.Taxa	Taxa-class
CalculateEfficiencyArray	CalculateEfficiencyArray
CalculateEfficiencyFISH	CalculateEfficiencyFISH
CalculateEfficiencyPCR	CalculateEfficiencyPCR
Clusterize	Clusterize
Codec	Codec
ConsensusSequence	ConsensusSequence
Cophenetic	Cophenetic
CorrectFrameshifts	CorrectFrameshifts
CreateChimeras	CreateChimeras
DB2Seqs	DB2Seqs
DECIPHER	DECIPHER-package
deltaGrules	deltaGrules
deltaGrulesRNA	deltaGrulesRNA
deltaHrules	deltaHrules
deltaHrulesRNA	deltaHrulesRNA
deltaSrules	deltaSrules
deltaSrulesRNA	deltaSrulesRNA
DesignArray	DesignArray
DesignPrimers	DesignPrimers
DesignProbes	DesignProbes
DesignSignatures	DesignSignatures
DetectRepeats	DetectRepeats
DigestDNA	DigestDNA
Disambiguate	Disambiguate
DistanceMatrix	DistanceMatrix
ExtractGenes	ExtractGenes
FindChimeras	FindChimeras
FindGenes	FindGenes
FindNonCoding	FindNonCoding
FindSynteny	FindSynteny
FormGroups	FormGroups
Genes-class	Genes-class
HEC_MI1	HEC_MI
HEC_MI2	HEC_MI
IdConsensus	IdConsensus
IdentifyByRank	IdentifyByRank
IdLengths	IdLengths
IdTaxa	IdTaxa
IndexSeqs	IndexSeqs
InferDemography	InferDemography
InferRecombination	InferRecombination
InferSelection	InferSelection
InvertedIndex-class	InvertedIndex-class
LearnNonCoding	LearnNonCoding
LearnTaxa	LearnTaxa
MapCharacters	MapCharacters
MaskAlignment	MaskAlignment
MeltDNA	MeltDNA
MIQS	MIQS
MMLSUM	MMLSUM
MODELS	MODELS
NNLS	NNLS
NonCoding-class	NonCoding-class
NonCodingRNA_Archaea	NonCodingRNA
NonCodingRNA_Bacteria	NonCodingRNA
NonCodingRNA_Eukarya	NonCodingRNA
OrientNucleotides	OrientNucleotides
pairs.Synteny	Synteny-class
PAM	PAM
PFASUM	PFASUM
plot.Genes	Genes-class
plot.Synteny	Synteny-class
plot.Taxa	Taxa-class
PredictDBN	PredictDBN
PredictHEC	PredictHEC
print.Genes	Genes-class
print.InvertedIndex	InvertedIndex-class
print.NonCoding	NonCoding-class
print.Synteny	Synteny-class
print.Taxa	Taxa-class
ReadDendrogram	ReadDendrogram
RemoveGaps	RemoveGaps
RESTRICTION_ENZYMES	RESTRICTION_ENZYMES
ScoreAlignment	ScoreAlignment
SearchDB	SearchDB
SearchIndex	SearchIndex
Seqs2DB	Seqs2DB
StaggerAlignment	StaggerAlignment
Synteny-class	Synteny-class
Taxa-class	Taxa-class
TerminalChar	TerminalChar
TileSeqs	TileSeqs
TrainingSet_16S	TrainingSet_16S
TreeLine	Treeline
Treeline	Treeline
TrimDNA	TrimDNA
WriteDendrogram	WriteDendrogram
WriteGenes	WriteGenes
[.Genes	Genes-class
[.Synteny	Synteny-class
[.Taxa	Taxa-class
