R: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

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

## Documentation for package ‘haplotypes’ version 1.1.3.2

- DESCRIPTION file
- Package README

## Help Pages

A B D G H I L N P R S T U misc

haplotypes-package | 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 --

image-method | Display DNA Sequence
image-methods | Display DNA Sequence
indelcoder | Codes gaps
indelcoder-method | Codes gaps
indelcoder-methods | Codes gaps

## -- 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'