aphid-package	aphid
align	align
align.AAbin	align
align.default	align
align.DNAbin	align
align.list	align
aphid	aphid
backward	backward
backward.HMM	backward
backward.PHMM	backward
casino	casino
deriveHMM	deriveHMM
derivePHMM	derivePHMM
derivePHMM.AAbin	derivePHMM
derivePHMM.default	derivePHMM
derivePHMM.DNAbin	derivePHMM
derivePHMM.list	derivePHMM
forward	forward
forward.HMM	forward
forward.PHMM	forward
generate	generate
generate.HMM	generate
generate.PHMM	generate
globins	globins
logsum	logsum
map	map
plot.HMM	plot.HMM
plot.PHMM	plot.PHMM
posterior	posterior
posterior.HMM	posterior
posterior.PHMM	posterior
print	print
print.DPA	print
print.HMM	print
print.PHMM	print
readPHMM	readPHMM
substitution	substitution
train	train
train.HMM	train
train.PHMM	train
unalign	unalign
Viterbi	Viterbi
Viterbi.default	Viterbi
Viterbi.HMM	Viterbi
Viterbi.PHMM	Viterbi
weight	weight
weight.AAbin	weight
weight.default	weight
weight.dendrogram	weight
weight.DNAbin	weight
weight.list	weight
writePHMM	writePHMM
