aa2selfscore	aa2selfscore
aabin2aastring	aabin2aastring
AAMatrix	AAMatrix-data
AAMatrix-data	AAMatrix-data
aastring2aabin	aastring2aabin
aastring2aln	aastring2aln
aastring2dist	aastring2dist
addmask2string	addmask2string
addpop2string	addpop2string
addpos2string	addpos2string
addregion2string	addregion2string
aln2aastring	aln2aastring
aln2dnastring	aln2dnastring
cds2aa	cds2aa
cds2codonaln	cds2codonaln
cdsstring2codonaln	cdsstring2codonaln
codon2number	GENETIC_CODE_TCAG
codon2numberAMBIG	codon2numberAMBIG
codon2numberTCAG	codon2numberTCAG
codonmat2pnps	codonmat2pnps
codonmat2xy	codonmat2xy
collapseChar	collapseChar
collapseXStringSet	collapseXStringSet
compareCodons	compareCodons
dist2dxy	dist2dxy
dnabin2dnastring	dnabin2dnastring
dnastring2aln	dnastring2aln
dnastring2codonmat	dnastring2codonmat
dnastring2dist	dnastring2dist
dnastring2dnabin	dnastring2dnabin
dnastring2dxy	dnastring2dxy
dnastring2kaks	dnastring2kaks
dnastring2weightedPi	dnastring2weightedPi
GENETIC_CODE_TCAG	GENETIC_CODE_TCAG
getmask	getmask
getpos	getpos
globalDeletion	globalDeletion
globalDeletionAA	globalDeletionAA
granthamMatrix	granthamMatrix
hiv	hiv-data
hiv-data	hiv-data
indices2kaks	indices2kaks
iupac	iupac-data
iupac-data	iupac-data
iupacMatrix	iupacMatrix
makePostalignedSeqs	makePostalignedSeqs
normpop	normpop
pal2nal	pal2nal
popinteger	popinteger
popnames	popnames
rcpp_distSTRING	rcpp_distSTRING
rcpp_dxy_fst_pop	rcpp_dxy_fst_pop
rcpp_KaKs	rcpp_KaKs
rcpp_pairwiseDeletionAA	rcpp_pairwiseDeletionAA
rcpp_pairwiseDeletionDNA	rcpp_pairwiseDeletionDNA
rcpp_weightedPi	rcpp_weightedPi
rcpp_weightedPi_pop	rcpp_weightedPi_pop
region	region
regionused	regionused
string2region	string2region
subString	subString
uptriidx	uptriidx
