Dna-class               Class '"Dna"' in the Package 'haplotypes'
Haplotype-class         Class '"Haplotype"' in the Package 'haplotypes'
Parsimnet-class         Class '"Parsimnet"' in the Package 'haplotypes'
[-methods               Extract or replace parts of an object of class
                        'Dna'
append-methods          Combines two 'Dna' objects
as.DNAbin-methods       Coerces an object to a 'DNAbin' object
as.data.frame-methods   Coerces a 'Dna' object to a data.frame
as.dna-methods          Coerces an object to a 'Dna' object
as.list-methods         Methods for function 'as.list' in the Package
                        'haplotypes'
as.matrix-methods       Methods for function 'as.matrix' in the Package
                        'haplotypes'
as.network-methods      Coerces an object to a 'network' object
as.networx-methods      Coerces an object to a 'networx' object
as.numeric-methods      Coerces a 'Dna' object to a numeric matrix
as.phyDat-methods       Coerces an object to a 'phyDat' object
basecomp-methods        Calculates base composition
boot.dna-methods        Generates single bootstrap replicate
distance-methods        Calculates absolute pairwise character
                        difference matrix using a 'Dna' object
dna.obj                 Example DNA sequence data
grouping-methods        Groups haplotypes according to the grouping
                        variable (populations, species, etc.)
haplotype-methods       Methods for function 'haplotype' in the package
                        'haplotypes'
haplotypes-package      Manipulating DNA Sequences and Estimating
                        Unambiguous Haplotype Network with Statistical
                        Parsimony
hapreord-methods        Reorders haplotypes according to the ordering
                        factor
homopoly-methods        Provides the list of homoplastic indels and
                        substitutions
image-methods           Display DNA Sequence
indelcoder-methods      Codes gaps
length-methods          Methods for function 'length' in the package
                        'haplotypes'
names-methods           Function to get or set names of a 'Dna' object
                        or 'Parsimnet' object
ncol-methods            Returns the length of the longest DNA sequence
nrow-methods            Returns the number of DNA sequences
pairPhiST-methods       Provides the pairwise PhiST between populations
pairnei-methods         Provides the average number of pairwise Nei's
                        (D) differences between populations
parsimnet-methods       Estimates gene genealogies using statistical
                        parsimony
pielegend-methods       Add Legends to Plots
pieplot-methods         Plots pie charts on statistical parsimony
                        network
plot-methods            Methods for function 'plot' in the package
                        'haplotypes'
polymorp-methods        Displays polymorphic sites (base substitutions
                        and indels) between two sequences
range-methods           Returns the minimum and maximum lengths of the
                        DNA sequences
read.fas                Read sequences from a file in FASTA format
remove.gaps-methods     Removing gaps from 'Dna' object
rownames-methods        Retrieve or set the row names
show-methods            Methods for function 'show' in the package
                        'haplotypes'
subs-methods            Displays base substitutions
tolower-methods         Convert sequence characters from upper to lower
                        case or vice versa
unique-methods          Extract Unique Sequences
