haplotypes
Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Package index
Search the haplotypes package
Vignettes
Functions
201
Source code
3
Man pages
45
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haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony
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API

API for haplotypes
Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Global functions
Dna Man page
Dna-class Man page
Haplotype Man page
Haplotype-class Man page
Parsimnet Man page
Parsimnet-class Man page
[,Dna,ANY,ANY,ANY-method Man page
[,Dna-method Man page
[-methods Man page
[<-,Dna,ANY,ANY,ANY-method Man page
[<-,Dna-method Man page
add.miss Man page
alltest Man page Source code
append,Dna-method Man page
append-methods Man page
as.DNAbin Man page
as.DNAbin,Dna-method Man page
as.DNAbin-methods Man page
as.data.frame,Dna-method Man page
as.data.frame-methods Man page
as.dna Man page
as.dna,DNAbin-method Man page
as.dna,Haplotype-method Man page
as.dna,character-method Man page
as.dna,data.frame-method Man page
as.dna,list-method Man page
as.dna,matrix-method Man page
as.dna,phyDat-method Man page
as.dna-methods Man page
as.list,Dna-method Man page
as.list,Haplotype-method Man page
as.list,Parsimnet-method Man page
as.list-methods Man page
as.matrix,Dna-method Man page
as.matrix-methods Man page
as.network Man page
as.network,Parsimnet-method Man page
as.network-methods Man page
as.networx Man page
as.networx,Parsimnet-method Man page
as.networx-methods Man page
as.numeric,Dna-method Man page
as.numeric-methods Man page
as.phyDat Man page
as.phyDat,Dna-method Man page
as.phyDat-methods Man page
as.sequence Man page
basecomp Man page
basecomp,Dna-method Man page
basecomp-methods Man page
boot.dna Man page
boot.dna,Dna-method Man page
boot.dna-methods Man page
calcclust Man page Source code
clsfyindels Man page
clustersG Man page Source code
contr Man page Source code
distance Man page
distance,Dna-method Man page
distance-methods Man page
distance2 Man page
dna.obj Man page
ext.nodes Man page Source code
fillendgaps Man page Source code
fillna Man page Source code
geodist.corr Man page Source code
grouping Man page
grouping,Haplotype-method Man page
grouping-methods Man page
haplo Man page Source code
haplotype Man page
haplotype,Dna-method Man page
haplotype,dist-method Man page
haplotype,matrix-method Man page
haplotype-methods Man page
haplotypes Man page
haplotypes-package Man page
hapreord Man page
hapreord,Haplotype-method Man page
hapreord-methods Man page
has.cycle Man page Source code
homopoly Man page
homopoly,Dna-method Man page
homopoly-methods Man page
image,Dna-method Man page
image-methods Man page
indelcoder Man page
indelcoder,Dna-method Man page
indelcoder-methods Man page
indtest Man page Source code
initialize,Dna-method Man page
initialize,Haplotype-method Man page
initialize,Parsimnet-method Man page
initialize-methods Man page
length,Dna-method Man page
length,Haplotype-method Man page
length,Parsimnet-method Man page
length-methods Man page
multipolypoz Man page
names,Dna-method Man page
names,Parsimnet-method Man page
names-methods Man page
names<-,Dna-method Man page
names<-,Parsimnet-method Man page
names<--methods Man page
ncol,Dna-method Man page
ncol-methods Man page
nrow,Dna-method Man page
nrow-methods Man page
pairPhiST Man page
pairPhiST,Dna-method Man page
pairPhiST,dist-method Man page
pairPhiST,matrix-method Man page
pairPhiST-methods Man page
pairPhiSTdist Man page Source code
pairnei Man page
pairnei,Dna-method Man page
pairnei,dist-method Man page
pairnei,matrix-method Man page
pairnei-methods Man page
pairneidist Man page Source code
parsimnet Man page
parsimnet,Dna-method Man page
parsimnet,dist-method Man page
parsimnet,matrix-method Man page
parsimnet-methods Man page
parsnet Man page Source code
pegas.amova Man page
pielegend Man page
pielegend,Parsimnet,Haplotype-method Man page
pielegend-methods Man page
pieplot Man page
pieplot,Parsimnet,Haplotype-method Man page
pieplot-methods Man page
plot,Parsimnet,missing-method Man page
plot,Parsimnet-method Man page
plot-methods Man page
polymorp Man page
polymorp,Dna-method Man page
polymorp-methods Man page
polys Man page
range,Dna-method Man page
range-methods Man page
read.fas Man page Source code
recdistG Man page Source code
remove.gaps Man page
remove.gaps,Dna-method Man page
remove.gaps-methods Man page
ren.dupli Man page Source code
ri Man page
rownames,Dna-method Man page
rownames,Parsimnet-method Man page
rownames-methods Man page
rownames<-,Dna-method Man page
rownames<-,Parsimnet-method Man page
rownames<--methods Man page
show,Dna-method Man page
show,Haplotype-method Man page
show,Parsimnet-method Man page
show-methods Man page
sic Man page Man page Source code
steplimit Man page Source code
subs Man page
subs,Dna-method Man page
subs-methods Man page
tolower,Dna-method Man page
tolower-methods Man page
toupper,Dna-method Man page
toupper-methods Man page
tryconnect Man page Source code
tryconnectG Man page Source code
unique,Dna,ANY-method Man page
unique,Dna-method Man page
unique-methods Man page
validity Man page Man page Source code
xhaps Man page Source code
haplotypes documentation built on Nov. 5, 2025, 5:36 p.m.

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