align.clustalw	align.clustalw
align.MEME	align.MEME
align.muscle	align.muscle
Alignment	Alignment
BackgroundOrganism	BackgroundOrganism
CalculInformation	CalculInformation
CalculPSSM	CalculPSSM
CalculPWM	CalculPWM
CalculRedundancy	CalculRedundancy
CalculScores	CalculScores
CalculSimilarity	CalculSimilarity
chooseModel	chooseModel
classMODEL	classMODEL
ConstructModel	ConstructModel
correction-class	correction
correction.entropy	correction.entropy
correction.redundancy	correction.redundancy
correctionaprox	correctionaprox
CreateConsensus	CreateConsensus
detection	detection
detector_1rOrdre_diff	detector_1rOrdre_diff
detector_2nOrdre	detector_2nOrdre
detector_2nOrdre_init	detector_2nOrdre_init
diffInstructions	diffInstructions
divergence.Renyi	divergence.Renyi
divergence.Shannon	divergence.Shannon
DivergenceDROSOPHILA	DivergenceDROSOPHILA
DivergenceHOMO	DivergenceHOMO
DivergenceMUS	DivergenceMUS
DivergenceRATTUS	DivergenceRATTUS
entropy.corrected	entropy.corrected
entropy.joint	entropy.joint
entropy.Renyi	entropy.Renyi
entropy.Shannon	entropy.Shannon
EntropyDROSOPHILA	EntropyDROSOPHILA
EntropyHOMO	EntropyHOMO
EntropyMUS	EntropyMUS
EntropyRATTUS	EntropyRATTUS
Hmemory	Hmemory
Hread	Hread
iicc	iicc
JacksonParameters	JacksonParameters
joint.probability	joint.probability
kfold.Divergence	kfold.Divergence
kfold.Entropy	kfold.Entropy
kfold.MATCH	kfold.MATCH
kfold.MDscan	kfold.MDscan
kfold.MEME	kfold.MEME
kfold.PCA	kfold.PCA
kfold.transMEME	kfold.transMEME
MEET	MEET
MImemory	MImemory
MIread	MIread
Model-class	Model
ModelDivergence	ModelDivergence
ModelEntropy	ModelEntropy
ModelMATCH	ModelMATCH
ModelMDscan	ModelMDscan
ModelMEME	ModelMEME
ModelPCA	ModelPCA
Models	Models
ModeltransMEME	ModeltransMEME
motif.mast	motif.mast
numericalDNA	numericalDNA
organism	organism
PCanalysis	PCanalysis
PredictDivergence	PredictDivergence
PredictEntropy	PredictEntropy
Prediction	Prediction
PredictMATCH	PredictMATCH
PredictMDscan	PredictMDscan
PredictMEME	PredictMEME
PredictPCA	PredictPCA
PredicttransMEME	PredicttransMEME
Prob	Prob
probability	probability
probability.couple	probability.couple
pvalue	pvalue
q	q
QresidualsDROSOPHILA	QresidualsDROSOPHILA
QresidualsHOMO	QresidualsHOMO
QresidualsMUS	QresidualsMUS
QresidualsRATTUS	QresidualsRATTUS
QtoJackson	QtoJackson
Read.aligned	Read.aligned
read.mast	read.mast
readMEME	readMEME
ReadSequence	ReadSequence
redundancy	redundancy
ROCmodel	ROCmodel
run.read.MDscan	run.read.MDscan
scoreMDscan	scoreMDscan
Sequence	Sequence
standardout	standardout
TFlogodds	TFlogodds
TranscriptionFactor	TranscriptionFactor
writeMEME	writeMEME
writeResultsHTML	writeResultsHTML
