pegas-package	pegas-package
all.equal.haploNet	all.equal.haploNet
alleles2loci	alleles2loci
allelicrichness	allelicrichness
amova	amova
as.evonet.haploNet	haploNet
as.igraph.haploNet	haploNet
as.loci	conversion
as.loci.character	conversion
as.loci.data.frame	conversion
as.loci.factor	conversion
as.loci.genind	conversion
as.loci.matrix	conversion
as.network.haploNet	haploNet
as.phylo.haploNet	haploNet
bind.loci	bind.loci
by.loci	by.loci
cbind.loci	bind.loci
cophenetic.haploNet	cophenetic.haploNet
diffHaplo	diffHaplo
dist.asd	dist.asd
dist.hamming	dist.hamming
dist.haplotype.loci	haplotype.loci
edit.loci	edit.loci
expand.genotype	utilities
F2	F234
F3	F234
F4	F234
Fst	Fst
genind2loci	conversion
geod	geod
geoTrans	geoTrans
geoTrans2	geoTrans
getAlleles	utilities
getGenotypes	utilities
getHaploNetOptions	options_themes_haploNet
getINFO	VCFloci
getPhi	amova
getPloidy	utilities
H	heterozygosity
H.default	heterozygosity
H.loci	heterozygosity
hap.div	hap.div
hap.div.DNAbin	hap.div
hap.div.haplotype	hap.div
haploFreq	haploFreq
haploNet	haploNet
haplotype	haplotype
haplotype.character	haplotype
haplotype.DNAbin	haplotype
haplotype.loci	haplotype.loci
haplotype.numeric	haplotype
heterozygosity	heterozygosity
hw.test	hw.test
hw.test.genind	hw.test
hw.test.loci	hw.test
is.phased	utilities
is.snp	utilities
is.snp.loci	utilities
is.snp.VCFinfo	VCFloci
jaguar	jaguar
LD	LD
LD2	LD
LDmap	LDscan
LDscan	LDscan
LDscan.DNAbin	LDscan
LDscan.loci	LDscan
lines.stairway	stairway
loci	read.loci
loci2alleles	alleles2loci
loci2genind	conversion
loci2SnpMatrix	conversion
mjn	mjn
MMD	MMD
msn	mst
mst	mst
mutations	mutations
na.omit.loci	na.omit.loci
nuc.div	nuc.div
nuc.div.DNAbin	nuc.div
nuc.div.haplotype	nuc.div
pegas	pegas-package
plot.haploNet	haploNet
plot.haplotype	haplotype
plot.haplotype.loci	haplotype.loci
plot.mjn	mjn
plot.spectrum	site.spectrum
plot.stairway	stairway
plot.summary.loci	summary.loci
plot.sw	sw
plotNetMDS	plotNetMDS
print.amova	amova
print.haploNet	haploNet
print.haplotype	haplotype
print.loci	summary.loci
print.summary.loci	summary.loci
print.VCFinfo	VCFloci
proba.genotype	utilities
R2.test	R2.test
rangePOS	VCFloci
rarefactionplot	allelicrichness
rbind.loci	bind.loci
read.gtx	read.gtx
read.loci	read.loci
read.vcf	read.vcf
replot	replot
rhost	allelicrichness
rmst	mst
rr.test	rr.test
Rst	Fst
selectQUAL	VCFloci
setHaploNetOptions	options_themes_haploNet
site.spectrum	site.spectrum
site.spectrum.DNAbin	site.spectrum
site.spectrum.loci	site.spectrum
sort.haplotype	haplotype
stairway	stairway
subset.haplotype	subset.haplotype
summary.haplotype	haplotype
summary.loci	summary.loci
sw	sw
sw.default	sw
sw.DNAbin	sw
tajima.test	tajima.test
theta.h	theta.h
theta.k	theta.k
theta.msat	theta.msat
theta.s	theta.s
theta.s.default	theta.s
theta.s.DNAbin	theta.s
theta.tree	theta.tree
theta.tree.hetero	theta.tree
unphase	utilities
VCFheader	VCFloci
VCFlabels	VCFloci
VCFloci	VCFloci
write.loci	write.loci
write.pegas.amova	amova
write.vcf	read.vcf
[.haplotype	haplotype
[.loci	summary.loci
