haplotypes-package	haplotypes-package
alltest	haplotypes-internal
append	append-methods
append,Dna-method	append-methods
append-methods	append-methods
as.data.frame	as.data.frame-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,data.frame-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-methods	as.dna-methods
as.list	as.list-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	as.matrix-methods
as.matrix,Dna-method	as.matrix-methods
as.matrix-methods	as.matrix-methods
as.numeric	as.numeric-methods
as.numeric,Dna-method	as.numeric-methods
as.numeric-methods	as.numeric-methods
calcclust	haplotypes-internal
clustersG	haplotypes-internal
distance	distance-methods
distance,Dna-method	distance-methods
distance-methods	distance-methods
Dna	Dna-class
Dna-class	Dna-class
dna.obj	dna.obj
fillendgaps	haplotypes-internal
fillna	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
indelcoder	indelcoder-methods
indelcoder,Dna-method	indelcoder-methods
indelcoder-methods	indelcoder-methods
initialize,Dna-method	haplotypes-internal
initialize,Haplotype-method	haplotypes-internal
initialize,Parsimnet-method	haplotypes-internal
initialize-methods	haplotypes-internal
length	length-methods
length,Dna-method	length-methods
length,Haplotype-method	length-methods
length,Parsimnet-method	length-methods
length-methods	length-methods
names	names-methods
names,Dna-method	names-methods
names-methods	names-methods
names<-,Dna-method	names-methods
names<--methods	names-methods
ncol	ncol-methods
ncol,Dna-method	ncol-methods
ncol-methods	ncol-methods
nrow	nrow-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
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
plot,Parsimnet-method	plot-methods
plot-methods	plot-methods
polymorp	polymorp-methods
polymorp,Dna-method	polymorp-methods
polymorp-methods	polymorp-methods
read.fas	read.fas
recdistG	haplotypes-internal
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
tryconnect	haplotypes-internal
tryconnectG	haplotypes-internal
validity	haplotypes-internal
xhaps	haplotypes-internal
[,Dna-method	z[-methods
[-methods	z[-methods
[<-,Dna-method	z[-methods
