aclust	aclust
AMPSequences	AMPSequences
AMPSequences.response	AMPSequences.response
BIC	BIC
BIC,MotifModel-method	MotifModel-class
BIC,MotifModelSet-method	MotifModelSet-class
blosum50	blosum50
blosum62	blosum62
blosum90	blosum90
changeClusterFormat	changeClusterFormat
classify	classify
classify,MotifModelSet-method	MotifModelSet-class
default.MetricParams	default.MetricParams
defaultBaseMatrix	defaultBaseMatrix
Descriptors	Descriptors-class
descriptors	Descriptors-class
Descriptors-class	Descriptors-class
dist,Sequences-method	Sequences
logLik,MotifModel-method	MotifModel-class
logLik,MotifModelSet-method	MotifModelSet-class
logLik,OOPS-method	MotifModel-class
logLik,SSOOPS-method	MotifModel-class
logLik,ZOOPS-method	MotifModel-class
MetricParams	MetricParams-class
MetricParams-class	MetricParams-class
MotifModel	MotifModel-class
motifModel	MotifModel-class
MotifModel-class	MotifModel-class
MotifModelSet	MotifModelSet-class
motifModelSet	MotifModelSet-class
MotifModelSet-class	MotifModelSet-class
motifString	MotifModel-class
motifString,MotifModel-method	MotifModel-class
plot,Descriptors-method	Descriptors-class
plot,MotifModel-method	MotifModel-class
plot,MotifModelSet-method	MotifModelSet-class
plot,Sequences-method	Sequences
plotFits	MotifModel-class
plotFits,MotifModel-method	MotifModel-class
plotPositions	MotifModel-class
plotPositions,MotifModel-method	MotifModel-class
plotStartingPosition	MotifModel-class
plotStartingPosition,MotifModel-method	MotifModel-class
predict,MotifModel-method	MotifModel-class
predict,MotifModelSet-method	MotifModelSet-class
print,MotifModel-method	MotifModel-class
rbind,Sequences-method	Sequences
read.fasta	read.fasta
read.sequences	read.sequences
residuals,MotifModel-method	MotifModel-class
residuals,MotifModelSet-method	MotifModelSet-class
Sequences	Sequences
Sequences-class	Sequences
SHP2Sequences	SHP2Sequences
simpleDescriptors	simpleDescriptors
TULASequences	TULASequences
write.fasta	write.fasta
write.sequences	write.sequences
[,Sequences-method	Sequences
