Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Documentation for package ‘haplotypes’ version 1.1.3.1

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Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

-- A --

append-method	Combines two 'Dna' objects
append-methods	Combines two 'Dna' objects
as.data.frame-method	Coerces a 'Dna' object to a data.frame
as.data.frame-methods	Coerces a 'Dna' object to a data.frame
as.dna	Coerces an object to a 'Dna' object
as.dna-method	Coerces an object to a 'Dna' object
as.dna-methods	Coerces an object to a 'Dna' object
as.DNAbin	Coerces an object to a 'DNAbin' object
as.DNAbin-method	Coerces an object to a 'DNAbin' object
as.DNAbin-methods	Coerces an object to a 'DNAbin' object
as.list-method	Methods for function 'as.list' in the Package 'haplotypes'
as.list-methods	Methods for function 'as.list' in the Package 'haplotypes'
as.matrix-method	Methods for function 'as.matrix' in the Package 'haplotypes'
as.matrix-methods	Methods for function 'as.matrix' in the Package 'haplotypes'
as.network	Coerces an object to a 'network' object
as.network-method	Coerces an object to a 'network' object
as.network-methods	Coerces an object to a 'network' object
as.networx	Coerces an object to a 'networx' object
as.networx-method	Coerces an object to a 'networx' object
as.networx-methods	Coerces an object to a 'networx' object
as.numeric-method	Coerces a 'Dna' object to a numeric matrix
as.numeric-methods	Coerces a 'Dna' object to a numeric matrix
as.phyDat	Coerces an object to a 'phyDat' object
as.phyDat-method	Coerces an object to a 'phyDat' object
as.phyDat-methods	Coerces an object to a 'phyDat' object

-- B --

basecomp	Calculates base composition
basecomp-method	Calculates base composition
basecomp-methods	Calculates base composition
boot.dna	Generates single bootstrap replicate
boot.dna-method	Generates single bootstrap replicate
boot.dna-methods	Generates single bootstrap replicate

-- D --

distance	Calculates absolute pairwise character difference matrix using a 'Dna' object
distance-method	Calculates absolute pairwise character difference matrix using a 'Dna' object
distance-methods	Calculates absolute pairwise character difference matrix using a 'Dna' object
Dna	Class '"Dna"' in the Package 'haplotypes'
Dna-class	Class '"Dna"' in the Package 'haplotypes'
dna.obj	Example DNA sequence data

-- G --

grouping	Groups haplotypes according to the grouping variable (populations, species, etc.)
grouping-method	Groups haplotypes according to the grouping variable (populations, species, etc.)
grouping-methods	Groups haplotypes according to the grouping variable (populations, species, etc.)

-- H --

Haplotype	Class '"Haplotype"' in the Package 'haplotypes'
haplotype	Methods for function 'haplotype' in the package 'haplotypes'
Haplotype-class	Class '"Haplotype"' in the Package 'haplotypes'
haplotype-method	Methods for function 'haplotype' in the package 'haplotypes'
haplotype-methods	Methods for function 'haplotype' in the package 'haplotypes'
haplotypes	Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony
hapreord	Reorders haplotypes according to the ordering factor
hapreord-method	Reorders haplotypes according to the ordering factor
hapreord-methods	Reorders haplotypes according to the ordering factor
homopoly	Provides the list of homoplastic indels and substitutions
homopoly-method	Provides the list of homoplastic indels and substitutions
homopoly-methods	Provides the list of homoplastic indels and substitutions

-- I --

-- L --

length-method	Methods for function 'length' in the package 'haplotypes'
length-methods	Methods for function 'length' in the package 'haplotypes'

-- N --

names-method	Function to get or set names of a 'Dna' object or 'Parsimnet' object
names-methods	Function to get or set names of a 'Dna' object or 'Parsimnet' object
names<--method	Function to get or set names of a 'Dna' object or 'Parsimnet' object
names<--methods	Function to get or set names of a 'Dna' object or 'Parsimnet' object
ncol-method	Returns the length of the longest DNA sequence
ncol-methods	Returns the length of the longest DNA sequence
nrow-method	Returns the number of DNA sequences
nrow-methods	Returns the number of DNA sequences

-- P --

pairnei	Provides the average number of pairwise Nei's (D) differences between populations
pairnei-method	Provides the average number of pairwise Nei's (D) differences between populations
pairnei-methods	Provides the average number of pairwise Nei's (D) differences between populations
pairPhiST	Provides the pairwise PhiST between populations
pairPhiST-method	Provides the pairwise PhiST between populations
pairPhiST-methods	Provides the pairwise PhiST between populations
Parsimnet	Class '"Parsimnet"' in the Package 'haplotypes'
parsimnet	Estimates gene genealogies using statistical parsimony
Parsimnet-class	Class '"Parsimnet"' in the Package 'haplotypes'
parsimnet-method	Estimates gene genealogies using statistical parsimony
parsimnet-methods	Estimates gene genealogies using statistical parsimony
pielegend	Add Legends to Plots
pielegend-method	Add Legends to Plots
pielegend-methods	Add Legends to Plots
pieplot	Plots pie charts on statistical parsimony network
pieplot-method	Plots pie charts on statistical parsimony network
pieplot-methods	Plots pie charts on statistical parsimony network
plot-method	Methods for function 'plot' in the package 'haplotypes'
plot-methods	Methods for function 'plot' in the package 'haplotypes'
polymorp	Displays polymorphic sites (base substitutions and indels) between two sequences
polymorp-method	Displays polymorphic sites (base substitutions and indels) between two sequences
polymorp-methods	Displays polymorphic sites (base substitutions and indels) between two sequences

-- R --

range-method	Returns the minimum and maximum lengths of the DNA 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	Removing gaps from 'Dna' object
remove.gaps-method	Removing gaps from 'Dna' object
remove.gaps-methods	Removing gaps from 'Dna' object
rownames-method	Retrieve or set the row names
rownames-methods	Retrieve or set the row names
rownames<--method	Retrieve or set the row names
rownames<--methods	Retrieve or set the row names

-- S --

show-method	Methods for function 'show' in the package 'haplotypes'
show-methods	Methods for function 'show' in the package 'haplotypes'
subs	Displays base substitutions
subs-method	Displays base substitutions
subs-methods	Displays base substitutions

-- T --

tolower-method	Convert sequence characters from upper to lower case or vice versa
tolower-methods	Convert sequence characters from upper to lower case or vice versa
toupper-method	Convert sequence characters from upper to lower case or vice versa
toupper-methods	Convert sequence characters from upper to lower case or vice versa

-- U --

unique-method	Extract Unique Sequences
unique-methods	Extract Unique Sequences

-- misc --

[-method	Extract or replace parts of an object of class 'Dna'
[-methods	Extract or replace parts of an object of class 'Dna'
[<--method	Extract or replace parts of an object of class 'Dna'