haplotypes-package	haplotypes-package
add.miss	haplotypes-internal
alltest	haplotypes-internal
append,Dna-method	append-methods
append-methods	append-methods
as.data.frame,Dna-method	as.data.frame-methods
as.data.frame-methods	as.data.frame-methods
as.dna	as.dna-methods
as.dna,character-method	as.dna-methods
as.dna,data.frame-method	as.dna-methods
as.dna,DNAbin-method	as.dna-methods
as.dna,Haplotype-method	as.dna-methods
as.dna,list-method	as.dna-methods
as.dna,matrix-method	as.dna-methods
as.dna,phyDat-method	as.dna-methods
as.dna-methods	as.dna-methods
as.DNAbin	as.DNAbin-methods
as.DNAbin,Dna-method	as.DNAbin-methods
as.DNAbin-methods	as.DNAbin-methods
as.list,Dna-method	as.list-methods
as.list,Haplotype-method	as.list-methods
as.list,Parsimnet-method	as.list-methods
as.list-methods	as.list-methods
as.matrix,Dna-method	as.matrix-methods
as.matrix-methods	as.matrix-methods
as.network	as.network-methods
as.network,Parsimnet-method	as.network-methods
as.network-methods	as.network-methods
as.networx	as.networx-methods
as.networx,Parsimnet-method	as.networx-methods
as.networx-methods	as.networx-methods
as.numeric,Dna-method	as.numeric-methods
as.numeric-methods	as.numeric-methods
as.phyDat	as.phyDat-methods
as.phyDat,Dna-method	as.phyDat-methods
as.phyDat-methods	as.phyDat-methods
as.sequence	haplotypes-internal
basecomp	basecomp-methods
basecomp,Dna-method	basecomp-methods
basecomp-methods	basecomp-methods
boot.dna	boot.dna-methods
boot.dna,Dna-method	boot.dna-methods
boot.dna-methods	boot.dna-methods
calcclust	haplotypes-internal
clsfyindels	haplotypes-internal
clustersG	haplotypes-internal
contr	haplotypes-internal
distance	distance-methods
distance,Dna-method	distance-methods
distance-methods	distance-methods
distance2	haplotypes-internal
Dna	Dna-class
Dna-class	Dna-class
dna.obj	dna.obj
ext.nodes	haplotypes-internal
fillendgaps	haplotypes-internal
fillna	haplotypes-internal
geodist.corr	haplotypes-internal
grouping	grouping-methods
grouping,Haplotype-method	grouping-methods
grouping-methods	grouping-methods
haplo	haplotypes-internal
Haplotype	Haplotype-class
haplotype	haplotype-methods
haplotype,dist-method	haplotype-methods
haplotype,Dna-method	haplotype-methods
haplotype,matrix-method	haplotype-methods
Haplotype-class	Haplotype-class
haplotype-methods	haplotype-methods
haplotypes	haplotypes-package
hapreord	hapreord-methods
hapreord,Haplotype-method	hapreord-methods
hapreord-methods	hapreord-methods
has.cycle	haplotypes-internal
homopoly	homopoly-methods
homopoly,Dna-method	homopoly-methods
homopoly-methods	homopoly-methods
image,Dna-method	image-methods
image-methods	image-methods
indelcoder	indelcoder-methods
indelcoder,Dna-method	indelcoder-methods
indelcoder-methods	indelcoder-methods
indtest	haplotypes-internal
initialize,Dna-method	haplotypes-internal
initialize,Haplotype-method	haplotypes-internal
initialize,Parsimnet-method	haplotypes-internal
initialize-methods	haplotypes-internal
length,Dna-method	length-methods
length,Haplotype-method	length-methods
length,Parsimnet-method	length-methods
length-methods	length-methods
multipolypoz	haplotypes-internal
names,Dna-method	names-methods
names,Parsimnet-method	names-methods
names-methods	names-methods
names<-,Dna-method	names-methods
names<-,Parsimnet-method	names-methods
names<--methods	names-methods
ncol,Dna-method	ncol-methods
ncol-methods	ncol-methods
nrow,Dna-method	nrow-methods
nrow-methods	nrow-methods
pairnei	pairnei-methods
pairnei,dist-method	pairnei-methods
pairnei,Dna-method	pairnei-methods
pairnei,matrix-method	pairnei-methods
pairnei-methods	pairnei-methods
pairneidist	haplotypes-internal
pairPhiST	pairPhiST-methods
pairPhiST,dist-method	pairPhiST-methods
pairPhiST,Dna-method	pairPhiST-methods
pairPhiST,matrix-method	pairPhiST-methods
pairPhiST-methods	pairPhiST-methods
pairPhiSTdist	haplotypes-internal
Parsimnet	Parsimnet-class
parsimnet	parsimnet-methods
parsimnet,dist-method	parsimnet-methods
parsimnet,Dna-method	parsimnet-methods
parsimnet,matrix-method	parsimnet-methods
Parsimnet-class	Parsimnet-class
parsimnet-methods	parsimnet-methods
parsnet	haplotypes-internal
pegas.amova	haplotypes-internal
pielegend	pielegend-methods
pielegend,Parsimnet,Haplotype-method	pielegend-methods
pielegend-methods	pielegend-methods
pieplot	pieplot-methods
pieplot,Parsimnet,Haplotype-method	pieplot-methods
pieplot-methods	pieplot-methods
plot,Parsimnet,missing-method	plot-methods
plot,Parsimnet-method	plot-methods
plot-methods	plot-methods
polymorp	polymorp-methods
polymorp,Dna-method	polymorp-methods
polymorp-methods	polymorp-methods
polys	haplotypes-internal
range,Dna-method	range-methods
range-methods	range-methods
read.fas	read.fas
recdistG	haplotypes-internal
remove.gaps	remove.gaps-methods
remove.gaps,Dna-method	remove.gaps-methods
remove.gaps-methods	remove.gaps-methods
ren.dupli	haplotypes-internal
ri	haplotypes-internal
rownames,Dna-method	rownames-methods
rownames,Parsimnet-method	rownames-methods
rownames-methods	rownames-methods
rownames<-,Dna-method	rownames-methods
rownames<-,Parsimnet-method	rownames-methods
rownames<--methods	rownames-methods
show,Dna-method	show-methods
show,Haplotype-method	show-methods
show,Parsimnet-method	show-methods
show-methods	show-methods
sic	haplotypes-internal
steplimit	haplotypes-internal
subs	subs-methods
subs,Dna-method	subs-methods
subs-methods	subs-methods
tolower,Dna-method	tolower-methods
tolower-methods	tolower-methods
toupper,Dna-method	tolower-methods
toupper-methods	tolower-methods
tryconnect	haplotypes-internal
tryconnectG	haplotypes-internal
unique,Dna,ANY-method	unique-methods
unique,Dna-method	unique-methods
unique-methods	unique-methods
validity	haplotypes-internal
xhaps	haplotypes-internal
[,Dna,ANY,ANY,ANY-method	z[-methods
[,Dna-method	z[-methods
[-methods	z[-methods
[<-,Dna,ANY,ANY,ANY-method	z[-methods
[<-,Dna-method	z[-methods
