adegenet.package-package	adegenet.package
$,genind-method	accessors
$,genlight-method	genlight
$,genpop-method	accessors
$,SNPbin-method	SNPbin
$<-,genind-method	accessors
$<-,genlight-method	genlight
$<-,genpop-method	accessors
$<-,SNPbin-method	SNPbin
.find.sub.clusters	find.clusters
.genlab	auxil
.readExt	auxil
.rmspaces	auxil
.valid.genind	genind
a.score	ascore
addStrata	strata-methods
addStrata,genind-method	strata-methods
addStrata,genlight-method	strata-methods
addStrata<-	strata-methods
addStrata<-,genind-method	strata-methods
addStrata<-,genlight-method	strata-methods
adegenet	adegenet.package
adegenet.package	adegenet.package
adegenetIssues	web
adegenetServer	servers
adegenetTutorial	web
adegenetWeb	web
alignment2genind	sequences
alleles	accessors
alleles,gen-method	accessors
alleles,genind-method	accessors
alleles,genlight-method	genlight
alleles,genpop-method	accessors
alleles<-	accessors
alleles<-,gen-method	accessors
alleles<-,genind-method	accessors
alleles<-,genlight-method	genlight
alleles<-,genpop-method	accessors
any2col	auxil
as,data.frame,genlight-method	genlight
as,genind,data.frame-method	as-methods
as,genind,genpop-method	as-methods
as,genind,ktab-method	as-methods
as,genind,matrix-method	as-methods
as,genlight,data.frame-method	as.genlight
as,genlight,list-method	as.genlight
as,genlight,matrix-method	as.genlight
as,genpop,data.frame-method	as-methods
as,genpop,ktab-method	as-methods
as,genpop,matrix-method	as-methods
as,integer,SNPbin-method	SNPbin
as,list,genlight-method	genlight
as,matrix,genlight-method	genlight
as,numeric,SNPbin-method	SNPbin
as,SNPbin,integer-method	as.SNPbin
as,SNPbin,numeric-method	as.SNPbin
as-method	as-methods
as.data.frame.genind	as-methods
as.data.frame.genlight	genlight
as.data.frame.genpop	as-methods
as.genind	new.genind
as.genlight	as.genlight
as.genlight,data.frame-method	as.genlight
as.genlight,list-method	as.genlight
as.genlight,matrix-method	as.genlight
as.genpop	new.genpop
as.genpop.genind	as-methods
as.igraph.haploGen	haploGen
as.igraph.seqTrack	seqTrack
as.integer.SNPbin	SNPbin
as.ktab.genind	as-methods
as.ktab.genpop	as-methods
as.lda	dapc
as.lda.dapc	dapc
as.list.genlight	genlight
as.matrix.genind	as-methods
as.matrix.genlight	genlight
as.matrix.genpop	as-methods
as.POSIXct.haploGen	haploGen
as.seqTrack.haploGen	haploGen
as.SNPbin	as.SNPbin
as.SNPbin,integer-method	as.SNPbin
as.SNPbin,numeric-method	as.SNPbin
assignplot	dapcGraphics
azur	auxil
bluepal	auxil
c.SNPbin	SNPbin
callOrNULL-class	virClasses
cbind.genlight	genlight
cbind.SNPbin	SNPbin
charOrNULL-class	virClasses
checkType	auxil
chooseCN	chooseCN
chr	genlight
chr,genlight-method	genlight
chr<-	genlight
chr<-,genlight-method	genlight
chromosome	genlight
chromosome,genlight-method	genlight
chromosome<-	genlight
chromosome<-,genlight-method	genlight
coerce,data.frame,genlight-method	genlight
coerce,genind,data.frame-method	as-methods
coerce,genind,genpop-method	as-methods
coerce,genind,ktab-method	as-methods
coerce,genind,matrix-method	as-methods
coerce,genlight,data.frame-method	as.genlight
coerce,genlight,list-method	as.genlight
coerce,genlight,matrix-method	as.genlight
coerce,genpop,data.frame-method	as-methods
coerce,genpop,ktab-method	as-methods
coerce,genpop,matrix-method	as-methods
coerce,integer,SNPbin-method	as.SNPbin
coerce,list,genlight-method	genlight
coerce,matrix,genlight-method	genlight
coerce,numeric,SNPbin-method	as.SNPbin
coerce,SNPbin,integer-method	SNPbin
colorplot	colorplot
colorplot.default	colorplot
colorplot.spca	spca
compoplot	dapcGraphics
coords.monmonier	coords.monmonier
corner	auxil
dapc	dapc
dapc.data.frame	dapc
dapc.dudi	dapc
dapc.genind	dapc
dapc.genlight	dapc
dapc.matrix	dapc
dapcIllus	dapcIllus
deepseasun	auxil
df2genind	df2genind
dfOrNULL-class	virClasses
dim,genlight-method	genlight
dist,genpop,ANY,ANY,ANY,missing-method	genpop
dist.genpop	dist.genpop
DNAbin2genind	sequences
eHGDP	eHGDP
extract.PLINKmap	read.PLINK
fac2col	auxil
factorOrNULL-class	virClasses
fasta2DNAbin	fasta2DNAbin
fasta2genlight	fasta2genlight
find.clusters	find.clusters
find.clusters.data.frame	find.clusters
find.clusters.genind	find.clusters
find.clusters.genlight	find.clusters
find.clusters.matrix	find.clusters
findMutations	mutations
findMutations.DNAbin	mutations
flame	auxil
formOrNULL-class	virClasses
funky	auxil
gen-class	virClasses
gengraph	gengraph
gengraph.default	gengraph
gengraph.dist	gengraph
gengraph.DNAbin	gengraph
gengraph.genind	gengraph
gengraph.genpop	gengraph
gengraph.matrix	gengraph
genind	new.genind
genind-class	genind
genind2df	genind2df
genind2genpop	genind2genpop
genlight	genlight
genlight-class	genlight
genpop	new.genpop
genpop-class	genpop
get.likelihood	seqTrack
get.likelihood.seqTrack	seqTrack
glDotProd	glAux
glMean	glAux
glNA	glAux
global.rtest	spca.rtests
glPca	glPca
glPlot	glPlot
glSim	glSim
glSum	glAux
glVar	glAux
graphMutations	mutations
graphMutations.DNAbin	mutations
greenpal	auxil
greypal	auxil
H3N2	H3N2
haploGen	haploGen
haploGen-class	haploGen
hier	hierarchy-methods
hier,genind-method	hierarchy-methods
hier,genlight-method	hierarchy-methods
hier<-	hierarchy-methods
hier<-,genind-method	hierarchy-methods
hier<-,genlight-method	hierarchy-methods
Hs	Hs
Hs.test	Hs.test
HWE.test.genind	HWE
hybridize	hybridize
import2genind	import2genind
inbreeding	inbreeding
indInfo-class	virClasses
indNames	accessors
indNames,genind-method	accessors
indNames,genlight-method	genlight
indNames<-	accessors
indNames<-,genind-method	accessors
indNames<-,genlight-method	genlight
initialize,genind-method	new.genind
initialize,genind-methods	new.genind
initialize,genlight-method	genlight
initialize,genpop-method	new.genpop
initialize,genpop-methods	new.genpop
initialize,SNPbin-method	SNPbin
intOrNULL-class	virClasses
intOrNum-class	virClasses
is.genind	genind
is.genpop	genpop
isPoly	isPoly
isPoly,genind-method	isPoly
isPoly,genpop-method	isPoly
isPoly-methods	isPoly
ktab-class	as-methods
labels.haploGen	haploGen
lightseasun	auxil
listOrNULL-class	virClasses
loadingplot	loadingplot
loadingplot.default	loadingplot
loadingplot.glPca	glPca
local.rtest	spca.rtests
locFac	accessors
locFac,gen-method	accessors
locFac,genind-method	accessors
locFac,genpop-method	accessors
locNames	accessors
locNames,gen-method	accessors
locNames,genind-method	accessors
locNames,genlight-method	genlight
locNames,genpop-method	accessors
locNames<-	accessors
locNames<-,gen-method	accessors
locNames<-,genind-method	accessors
locNames<-,genlight-method	genlight
locNames<-,genpop-method	accessors
makefreq	makefreq
makefreq,genind-method	makefreq
makefreq,genind-methods	makefreq
makefreq,genpop-method	makefreq
makefreq,genpop-methods	makefreq
microbov	microbov
minorAllele	minorAllele
monmonier	monmonier
NA.posi	genlight
NA.posi,genlight-method	genlight
NA.posi,SNPbin-method	SNPbin
nAll	accessors
nAll,gen-method	accessors
nAll,genind-method	accessors
nAll,genpop-method	accessors
names,genind-method	genind
names,genlight-method	genlight
names,genpop-method	genpop
names,SNPbin-method	SNPbin
nameStrata	strata-methods
nameStrata,genind-method	strata-methods
nameStrata,genlight-method	strata-methods
nameStrata<-	strata-methods
nameStrata<-,genind-method	strata-methods
nameStrata<-,genlight-method	strata-methods
nancycats	nancycats
nInd	accessors
nInd,genind-method	accessors
nInd,genlight-method	genlight
nLoc	accessors
nLoc,gen-method	accessors
nLoc,genind-method	accessors
nLoc,genlight-method	genlight
nLoc,genpop-method	accessors
nLoc,SNPbin-method	SNPbin
nPop	accessors
nPop,genind-method	accessors
nPop,genlight-method	genlight
nPop,genpop-method	accessors
num2col	auxil
old2new	old2new
old2new_genind	old2new
old2new_genlight	old2new
old2new_genpop	old2new
optim.a.score	ascore
optimize.monmonier	monmonier
other	accessors
other,gen-method	accessors
other,genind-method	accessors
other,genlight-method	genlight
other,genpop-method	accessors
other<-	accessors
other<-,gen-method	accessors
other<-,genind-method	accessors
other<-,genlight-method	genlight
other<-,genpop-method	accessors
pairDist	pairDist
pairDist.default	pairDist
pairDistPlot	pairDist
pairDistPlot.default	pairDist
pairDistPlot.dist	pairDist
pairDistPlot.DNAbin	pairDist
pairDistPlot.genind	pairDist
pairDistPlot.matrix	pairDist
ploidy	accessors
ploidy,genind-method	accessors
ploidy,genlight-method	genlight
ploidy,genpop-method	accessors
ploidy,SNPbin-method	SNPbin
ploidy<-	accessors
ploidy<-,genind-method	accessors
ploidy<-,genlight-method	genlight
ploidy<-,genpop-method	accessors
ploidy<-,SNPbin-method	SNPbin
plot,genlight,ANY-method	glPlot
plot,genlight-method	glPlot
plot.genlight	glPlot
plot.haploGen	haploGen
plot.monmonier	monmonier
plot.seqTrack	seqTrack
plot.spca	spca
plotHaploGen	haploGen
plotSeqTrack	seqTrack
pop	accessors
pop,genind-method	accessors
pop,genlight-method	genlight
pop<-	accessors
pop<-,gen-method	accessors
pop<-,genind-method	accessors
pop<-,genlight-method	genlight
popInfo-class	virClasses
popNames	accessors
popNames,genind-method	accessors
popNames,genlight-method	genlight
popNames,genpop-method	accessors
popNames<-	accessors
popNames<-,genind-method	accessors
popNames<-,genlight-method	genlight
popNames<-,genpop-method	accessors
position	genlight
position,genlight-method	genlight
position<-	genlight
position<-,genlight-method	genlight
predict.dapc	dapc
print,genind-method	genind
print,genindSummary-method	genind
print,genpopSummary-method	genpop
print.dapc	dapc
print.genindSummary	genind
print.genpopSummary	genpop
print.glPca	glPca
print.haploGen	haploGen
print.monmonier	monmonier
print.spca	spca
propShared	propShared
propTyped	propTyped
propTyped,genind-method	propTyped
propTyped,genpop-method	propTyped
propTyped-methods	propTyped
rbind.genlight	genlight
read.fstat	read.fstat
read.genepop	read.genepop
read.genetix	read.genetix
read.PLINK	read.PLINK
read.plink	read.PLINK
read.snp	read.snp
read.structure	read.structure
redpal	auxil
repool	repool
rupica	rupica
sample.haploGen	haploGen
scaleGen	scaleGen
scaleGen,genind-method	scaleGen
scaleGen,genpop-method	scaleGen
scaleGen-methods	scaleGen
scatter.dapc	dapcGraphics
scatter.glPca	glPca
screeplot.spca	spca
seasun	auxil
selPopSize	selpopsize
selPopSize,ANY-method	selpopsize
selPopSize,genind-method	selpopsize
selPopSize-methods	selpopsize
seploc	seploc
seploc,ANY-method	seploc
seploc,genind-method	seploc
seploc,genlight-method	seploc
seploc,genpop-method	seploc
seploc-methods	seploc
seppop	seppop
seppop,ANY-method	seppop
seppop,genind-method	seppop
seppop,genlight-method	seppop
seppop-methods	seppop
seqTrack	seqTrack
seqTrack-class	seqTrack
seqTrack.default	seqTrack
seqTrack.haploGen	haploGen
seqTrack.matrix	seqTrack
setPop	population-methods
setPop,genind-method	population-methods
setPop,genlight-method	population-methods
setPop<-	population-methods
setPop<-,genind-method	population-methods
setPop<-,genlight-method	population-methods
show,genind-method	genind
show,genlight-method	genlight
show,genpop-method	genpop
show,SNPbin-method	SNPbin
sim2pop	sim2pop
SNPbin	SNPbin
SNPbin-class	SNPbin
snpposi.plot	snpposi
snpposi.plot.DNAbin	snpposi
snpposi.plot.integer	snpposi
snpposi.plot.numeric	snpposi
snpposi.test	snpposi
snpposi.test.DNAbin	snpposi
snpposi.test.integer	snpposi
snpposi.test.numeric	snpposi
snpzip	snpzip
spca	spca
spcaIllus	spcaIllus
spectral	auxil
splitStrata	strata-methods
splitStrata,genind-method	strata-methods
splitStrata,genlight-method	strata-methods
splitStrata<-	strata-methods
splitStrata<-,genind-method	strata-methods
splitStrata<-,genlight-method	strata-methods
strata	strata-methods
strata,genind-method	strata-methods
strata,genlight-method	strata-methods
strata<-	strata-methods
strata<-,genind-method	strata-methods
strata<-,genlight-method	strata-methods
summary,genind-method	genind
summary,genpop-method	genpop
summary.dapc	dapc
summary.spca	spca
tab	tab
tab,genind-method	tab
tab,genind-methods	tab
tab,genpop-method	tab
tab,genpop-methods	tab
transp	auxil
truenames	truenames
truenames,ANY-method	truenames
truenames,genind-method	truenames
truenames,genpop-method	truenames
truenames-methods	truenames
USflu	H3N2
usflu	H3N2
USflu.fasta	H3N2
usflu.fasta	H3N2
wasp	auxil
xvalDapc	xvalDapc
xvalDapc.data.frame	xvalDapc
xvalDapc.matrix	xvalDapc
[,genind,ANY,ANY,ANY-method	accessors
[,genind-method	accessors
[,genlight,ANY,ANY,ANY-method	genlight
[,genlight,ANY,ANY-method	genlight
[,genlight-method	genlight
[,genpop,ANY,ANY,ANY-method	accessors
[,genpop-method	accessors
[,SNPbin,ANY,ANY,ANY-method	SNPbin
[,SNPbin,ANY,ANY-method	SNPbin
[,SNPbin-method	SNPbin
[.haploGen	haploGen