API for pegas
Population and Evolutionary Genetics Analysis System

Global functions
.TempletonProb	Source code
.VCFconnection	Source code
.bySNP	Source code
.check.order.alleles	Source code
.checkPloidy	Source code
.diffHaplo.loci	Source code
.drawAlternativeLinks	Source code
.drawSymbolsHaploNet	Source code
.eq13.Hurlbert1971	Source code
.getMETAvcf	Source code
.labelSegmentsHaploNet	Source code
.multinomialCoef	Source code
.mutationRug	Source code
.rotateSquares	Source code
.setWindow4haploNet	Source code
.sort.alleles	Source code
.squarePegas	Source code
F2	Man page Source code
F3	Man page Source code
F4	Man page Source code
Fst	Man page Source code
H	Man page Source code
H.default	Man page Source code
H.loci	Man page Source code
LD	Man page Source code
LD2	Man page Source code
LDmap	Man page Source code
LDscan	Man page Source code
LDscan.DNAbin	Man page Source code
LDscan.loci	Man page Source code
MMD	Man page Source code
R2.test	Man page Source code
Rst	Man page Source code
VCFheader	Man page Source code
VCFlabels	Man page Source code
VCFloci	Man page Source code
[.haplotype	Man page
[.loci	Man page
all.equal.haploNet	Man page Source code
alleles2loci	Man page Source code
allelicrichness	Man page Source code
amova	Man page Source code
as.evonet.haploNet	Man page Source code
as.igraph.haploNet	Man page Source code
as.loci	Man page Source code
as.loci.character	Man page Source code
as.loci.data.frame	Man page Source code
as.loci.factor	Man page Source code
as.loci.genind	Man page Source code
as.loci.matrix	Man page Source code
as.network.haploNet	Man page Source code
as.phylo.haploNet	Man page Source code
bind.loci	Man page
by.loci	Man page Source code
cbind.loci	Man page Source code
circle	Source code
cophenetic.haploNet	Man page Source code
diamond	Source code
diffHaplo	Man page Source code
dist.asd	Man page Source code
dist.hamming	Man page Source code
dist.haplotype.loci	Man page Source code
edit.loci	Man page Source code
expand.genotype	Man page Source code
genind2loci	Man page Source code
geoTrans	Man page Source code
geoTrans2	Man page Source code
geod	Man page Source code
getAllCombs	Source code
getAlleles	Man page Source code
getGenotypes	Man page Source code
getHaploNetOptions	Man page Source code
getINFO	Man page Source code
getPhi	Man page Source code
getPloidy	Man page Source code
hap.div	Man page Source code
hap.div.DNAbin	Man page Source code
hap.div.haplotype	Man page Source code
haploFreq	Man page Source code
haploNet	Man page Source code
haplotype	Man page Source code
haplotype.DNAbin	Man page Source code
haplotype.character	Man page Source code
haplotype.loci	Man page Source code
haplotype.numeric	Man page Source code
heterozygosity	Man page Source code
hw.test	Man page
hw.test.genind	Man page Source code
hw.test.loci	Man page Source code
is.phased	Man page Source code
is.snp	Man page Source code
is.snp.VCFinfo	Man page Source code
is.snp.loci	Man page Source code
jaguar	Man page
labels.haploNet	Source code
lines.stairway	Man page Source code
loci	Man page
loci2SnpMatrix	Man page Source code
loci2alleles	Man page Source code
loci2genind	Man page Source code
mjn	Man page Source code
msn	Man page Source code
mst	Man page Source code
mutations	Man page Source code
na.omit.loci	Man page Source code
nuc.div	Man page Source code
nuc.div.DNAbin	Man page Source code
nuc.div.haplotype	Man page Source code
nullAlleles2NA	Man page Source code
pegas	Man page
pegas-package	Man page
plot.haploNet	Man page Source code
plot.haplotype	Man page Man page Source code
plot.haplotype.loci	Man page Source code
plot.mjn	Man page Source code
plot.spectrum	Man page Source code
plot.stairway	Man page Source code
plot.summary.loci	Man page Source code
plot.sw	Man page Source code
plotNetMDS	Man page Source code
print.VCFinfo	Man page Source code
print.amova	Man page Source code
print.haploNet	Man page Source code
print.haplotype	Man page Source code
print.loci	Man page Source code
print.summary.loci	Man page Source code
proba.genotype	Man page Source code
rangePOS	Man page Source code
rarefactionplot	Man page Source code
rbind.loci	Man page Source code
read.gtx	Man page Source code
read.loci	Man page Source code
read.vcf	Man page Source code
replot	Man page Source code
rhost	Man page Source code
rmst	Man page Source code
rr.test	Man page Source code
selectQUAL	Man page Source code
setHaploNetOptions	Man page Source code
site.spectrum	Man page Source code
site.spectrum.DNAbin	Man page Source code
site.spectrum.loci	Man page Source code
sort.haplotype	Man page Source code
square	Source code
stairway	Man page Source code
subset.haplotype	Man page Source code
summary.haplotype	Man page Source code
summary.loci	Man page Source code
sw	Man page Source code
sw.DNAbin	Man page Source code
sw.default	Man page Source code
tajima.test	Man page Source code
theta.h	Man page Source code
theta.k	Man page Source code
theta.msat	Man page Source code
theta.s	Man page Source code
theta.s.DNAbin	Man page Source code
theta.s.default	Man page Source code
theta.tree	Man page Source code
theta.tree.hetero	Man page Source code
unphase	Man page Source code
write.loci	Man page Source code
write.pegas.amova	Man page Source code
write.vcf	Man page Source code