AAMultipleAlignment	MultipleAlignment-class
AAMultipleAlignment-class	MultipleAlignment-class
alphabetFrequency,MultipleAlignment-method	MultipleAlignment-utils
as.character,MultipleAlignment-method	MultipleAlignment-class
as.matrix,MultipleAlignment-method	MultipleAlignment-class
class:AAMultipleAlignment	MultipleAlignment-class
class:DNAMultipleAlignment	MultipleAlignment-class
class:MultipleAlignment	MultipleAlignment-class
class:RNAMultipleAlignment	MultipleAlignment-class
coerce,character,AAMultipleAlignment-method	MultipleAlignment-class
coerce,character,DNAMultipleAlignment-method	MultipleAlignment-class
coerce,character,RNAMultipleAlignment-method	MultipleAlignment-class
coerce,MultipleAlignment,AAStringSet-method	MultipleAlignment-class
coerce,MultipleAlignment,BStringSet-method	MultipleAlignment-class
coerce,MultipleAlignment,DNAStringSet-method	MultipleAlignment-class
coerce,MultipleAlignment,RNAStringSet-method	MultipleAlignment-class
colmask	MultipleAlignment-class
colmask,MultipleAlignment-method	MultipleAlignment-class
colmask<-	MultipleAlignment-class
colmask<-,MultipleAlignment,ANY-method	MultipleAlignment-class
colmask<-,MultipleAlignment,NULL-method	MultipleAlignment-class
consensusMatrix,MultipleAlignment-method	MultipleAlignment-utils
consensusString,AAMultipleAlignment-method	MultipleAlignment-utils
consensusString,DNAMultipleAlignment-method	MultipleAlignment-utils
consensusString,MultipleAlignment-method	MultipleAlignment-utils
consensusString,RNAMultipleAlignment-method	MultipleAlignment-utils
consensusViews	MultipleAlignment-utils
consensusViews,AAMultipleAlignment-method	MultipleAlignment-utils
consensusViews,DNAMultipleAlignment-method	MultipleAlignment-utils
consensusViews,MultipleAlignment-method	MultipleAlignment-utils
consensusViews,RNAMultipleAlignment-method	MultipleAlignment-utils
detail	detail
detail,MultipleAlignment-method	MultipleAlignment-class
dim,MultipleAlignment-method	MultipleAlignment-class
DNAMultipleAlignment	MultipleAlignment-class
DNAMultipleAlignment-class	MultipleAlignment-class
maskeddim	MultipleAlignment-class
maskeddim,MultipleAlignment-method	MultipleAlignment-class
maskedncol	MultipleAlignment-class
maskedncol,MultipleAlignment-method	MultipleAlignment-class
maskednrow	MultipleAlignment-class
maskednrow,MultipleAlignment-method	MultipleAlignment-class
maskedratio,MultipleAlignment-method	MultipleAlignment-class
maskGaps	MultipleAlignment-class
maskGaps,MultipleAlignment-method	MultipleAlignment-class
maskMotif,MultipleAlignment,ANY-method	MultipleAlignment-class
MultipleAlignment	MultipleAlignment-class
MultipleAlignment-class	MultipleAlignment-class
MultipleAlignment-IO	MultipleAlignment-IO
MultipleAlignment-utils	MultipleAlignment-utils
MultipleAlignment_IO	MultipleAlignment-IO
MultipleAlignment_utils	MultipleAlignment-utils
nchar,MultipleAlignment-method	MultipleAlignment-class
ncol,MultipleAlignment-method	MultipleAlignment-class
nrow,MultipleAlignment-method	MultipleAlignment-class
readAAMultipleAlignment	MultipleAlignment-IO
readDNAMultipleAlignment	MultipleAlignment-IO
readRNAMultipleAlignment	MultipleAlignment-IO
RNAMultipleAlignment	MultipleAlignment-class
RNAMultipleAlignment-class	MultipleAlignment-class
rowmask	MultipleAlignment-class
rowmask,MultipleAlignment-method	MultipleAlignment-class
rowmask<-	MultipleAlignment-class
rowmask<-,MultipleAlignment,ANY-method	MultipleAlignment-class
rowmask<-,MultipleAlignment,NULL-method	MultipleAlignment-class
rownames,MultipleAlignment-method	MultipleAlignment-class
rownames<-,MultipleAlignment-method	MultipleAlignment-class
seqtype,MultipleAlignment-method	MultipleAlignment-class
show,MultipleAlignment-method	MultipleAlignment-class
unmasked,MultipleAlignment-method	MultipleAlignment-class
updateObject,AAMultipleAlignment-method	MultipleAlignment-class
updateObject,DNAMultipleAlignment-method	MultipleAlignment-class
updateObject,RNAMultipleAlignment-method	MultipleAlignment-class
write.phylip	MultipleAlignment-IO
