strataG-package	strataG-package
.getFileLabel	strataG-internal
.parseLocusNames	strataG-internal
.setupClusters	strataG-internal
.strataPairs	strataG-internal
.writeArlequinHeader	write.arlequin
.writeArlequinMsats	write.arlequin
.writeArlequinSequences	write.arlequin
.writeArlequinStructure	write.arlequin
accessors	gtypes.accessors
alleleFreqFormat	alleleFreqFormat
alleleFreqs	alleleFreqs
alleleNames	gtypes.accessors
alleleNames,gtypes-method	gtypes.accessors
alleleSplit	alleleSplit
allelicRichness	allelicRichness
arlequin	write.arlequin
as.data.frame	as.data.frame.gtypes
as.data.frame,gtypes-method	as.data.frame.gtypes
as.data.frame.gtypes	as.data.frame.gtypes
as.matrix	as.matrix-gtypes-method
as.matrix,gtypes-method	as.matrix-gtypes-method
as.matrix.gtypes	as.matrix-gtypes-method
as.multidna	as.multidna
baseFreqs	baseFreqs
bowhead.snp.position	bowhead.snp.position
bowhead.snps	bowhead.snps
clumpp	clumpp
createConsensus	createConsensus
dA	nucleotideDivergence
description	gtypes.accessors
description,gtypes-method	gtypes.accessors
df2gtypes	df2gtypes
dloop.g	dloop.g
dolph.haps	dolph.haps
dolph.msats	dolph.msats
dolph.seqs	dolph.seqs
dolph.strata	dolph.strata
dupGenotypes	dupGenotypes
evanno	evanno
expectedNumAlleles	expectedNumAlleles
exptdHet	heterozygosity
fasta	fasta
fastsimcoal	fastsimcoal
fastsimcoal.input	fastsimcoal.input
fixedDifferences	fixedDifferences
fixedSites	fixedSites
freq2GenData	freq2GenData
fscHistEv	fastsimcoal.input
fscLocusParams	fastsimcoal.input
fscPopInfo	fastsimcoal.input
fscRead	fastsimcoal
fscWrite	fastsimcoal
fstToNm	fstToNm
fusFs	fusFs
gelato	gelato
gelatoPlot	gelato
genepop	genepop
genepopWrite	genepop
genind2gtypes	gtypes2genind
gtypes	gtypes-class
gtypes-class	gtypes-class
gtypes.accessors	gtypes.accessors
gtypes2genind	gtypes2genind
gtypes2loci	gtypes2loci
gtypes2phyDat	gtypes2phyDat
haplotypeLikelihoods	haplotypeLikelihoods
heterozygosity	heterozygosity
Hstats	popStructStat
HWE	hweTest
hwe	hweTest
hweTest	hweTest
idRows	idRows
index	gtypes.accessors
indNames	gtypes.accessors
indNames,gtypes-method	gtypes.accessors
initialize,gtypes-method	initialize-gtypes-method
initialize.gtypes	initialize-gtypes-method
is.gtypes	is.gtypes
isTi	TiTvRatio
isTv	TiTvRatio
iupacCode	iupacCode
jackHWE	jackHWE
jackInfluential	jackHWE
labelHaplotypes	labelHaplotypes
labelHaplotypes.default	labelHaplotypes
labelHaplotypes.gtypes	labelHaplotypes
LDgenepop	LDgenepop
loci	gtypes.accessors
loci,gtypes-method	gtypes.accessors
loci2gtypes	gtypes2loci
locNames	gtypes.accessors
locNames,gtypes-method	gtypes.accessors
lowFreqSubs	lowFreqSubs
mafft	mafft
MEGA	mega
mega	mega
mega,	mega
mostDistantSequences	mostDistantSequences
mostRepresentativeSequences	mostRepresentativeSequences
mRatio	mRatio
msats.g	msats.g
neiDa	neiDa
new	initialize-gtypes-method
nInd	gtypes.accessors
nInd,gtypes-method	gtypes.accessors
nLoc	gtypes.accessors
nLoc,gtypes-method	gtypes.accessors
nStrata	gtypes.accessors
nStrata,gtypes-method	gtypes.accessors
nucleotideDivergence	nucleotideDivergence
nucleotideDiversity	nucleotideDiversity
numAlleles	numAlleles
numGensEq	numGensEq
numMissing	numMissing
obsvdHet	heterozygosity
other	gtypes.accessors
other,gtypes-method	gtypes.accessors
overallTest	popStructTest
pairwiseTest	popStructTest
permuteStrata	permuteStrata
phase	phase
phaseFilter	phase
phasePosterior	phase
phaseReadPair	phase
phaseReadSample	phase
phaseWrite	phase
phyDat2gtypes	gtypes2phyDat
ploidy	gtypes.accessors
ploidy,gtypes-method	gtypes.accessors
plot.jack.influential	jackHWE
popStructStat	popStructStat
popStructTest	popStructTest
print.gtypeSummary	summary-gtypes-method
privateAlleles	privateAlleles
propSharedIds	sharedLoci
propSharedLoci	sharedLoci
propUniqueAlleles	propUniqueAlleles
qaqc	qaqc
read.fasta	fasta
read.mega	mega
readGenData	readGenData
removeSequences	removeSequences
schemes	gtypes.accessors
schemes,gtypes-method	gtypes.accessors
schemes<-	gtypes.accessors
schemes<-,gtypes-method	gtypes.accessors
sequence2gtypes	sequence2gtypes
sequences	gtypes.accessors
sequences,gtypes-method	gtypes.accessors
sharedAlleles	sharedLoci
sharedLoci	sharedLoci
show,gtypes-method	show-gtypes-method
show.gtypes	show-gtypes-method
simGammaHaps	simGammaHaps
statChi2	popStructStat
statFis	popStructStat
statFst	popStructStat
statFstPrime	popStructStat
statGst	popStructStat
statGstDblPrime	popStructStat
statGstPrime	popStructStat
statJostD	popStructStat
statList	popStructTest
statPhist	popStructStat
strata	gtypes.accessors
strata,gtypes-method	gtypes.accessors
strata<-	gtypes.accessors
strata<-,gtypes-method	gtypes.accessors
strataG	strataG-package
strataG-internal	strataG-internal
strataNames	gtypes.accessors
strataNames,gtypes-method	gtypes.accessors
strataSplit	strataSplit
stratify	stratify
structure	structure
structurePlot	structurePlot
structureRead	structure
structureRun	structure
structureWrite	structure
subset	gtypes.accessors
subType	TiTvRatio
summarizeLoci	summarizeLoci
summarizeSeqs	summarizeSeqs
summary	summary-gtypes-method
summary,gtypes-method	summary-gtypes-method
tajimasD	tajimasD
theta	theta
TiTvRatio	TiTvRatio
trimNs	trimNs
validIupacCodes	validIupacCodes
variableSites	variableSites
wrightFst	wrightFst
write.arlequin	write.arlequin
write.fasta	fasta
write.gtypes	write.gtypes
write.mega	mega
write.nexus.snapp	write.nexus.snapp
[,gtypes,ANY,ANY,ANY-method	gtypes.accessors
