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.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.numeric-methods      Coerces a 'Dna' object to a numeric matrix
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      Haplotype inference and statistical analysis of
                        genetic variation
hapreord-methods        Reorders haplotypes according to the ordering
                        factor
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
ncol-methods            Returns the length of the longest DNA sequence
nrow-methods            Returns the number of DNA sequences
pairnei-methods         Provides the average number of pairwise Nei's
                        (D) differences between populations
parsimnet-methods       Estimates gene genealogies using statistical
                        parsimony
plot-methods            Methods for function 'plot' in the package
                        'haplotypes'
polymorp-methods        Displays polymorphic sites (base substitutions
                        and indels) between two sequences
read.fas                Read sequences from a file in FASTA format
show-methods            Methods for function 'show' in the package
                        'haplotypes'
subs-methods            Displays base substitutions
