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haplotypes (version 1.1.3.2)

Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Description

Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel-coding method (only simple indel-coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and collapsing identical DNA sequences into haplotypes or inferring haplotypes using user-provided absolute pairwise character difference matrix. This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony and plotting parsimony networks.

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Version

Install

install.packages('haplotypes')

Monthly Downloads

994

Version

1.1.3.2

License

GPL-2

Maintainer

Caner Aktas

Last Published

October 6th, 2025

Functions in haplotypes (1.1.3.2)

basecomp-methods

Calculates base composition
grouping-methods

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

Methods for function length in the package haplotypes
haplotypes-package

Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony
ncol-methods

Returns the length of the longest DNA sequence
pairPhiST-methods

Provides the pairwise PhiST between populations
indelcoder-methods

Codes gaps
image-methods

Display DNA Sequence
names-methods

Function to get or set names of a Dna object or Parsimnet object
hapreord-methods

Reorders haplotypes according to the ordering factor
nrow-methods

Returns the number of DNA sequences
remove.gaps-methods

Removing gaps from Dna object
homopoly-methods

Provides the list of homoplastic indels and substitutions
range-methods

Returns the minimum and maximum lengths of the DNA sequences
read.fas

Read sequences from a file in FASTA format
rownames-methods

Retrieve or set the row names
plot-methods

Methods for function plot in the package haplotypes
pieplot-methods

Plots pie charts on statistical parsimony network
pairnei-methods

Provides the average number of pairwise Nei's (D) differences between populations
polymorp-methods

Displays polymorphic sites (base substitutions and indels) between two sequences
tolower-methods, toupper-methods

Convert sequence characters from upper to lower case or vice versa
pielegend-methods

Add Legends to Plots
unique-methods

Extract Unique Sequences
subs-methods

Displays base substitutions
parsimnet-methods

Estimates gene genealogies using statistical parsimony
show-methods

Methods for function show in the package haplotypes
[-methods

Extract or replace parts of an object of class Dna
as.matrix-methods

Methods for function as.matrix in the Package haplotypes
append-methods

Combines two Dna objects
as.dna-methods

Coerces an object to a Dna object
as.DNAbin-methods

Coerces an object to a DNAbin object
as.data.frame-methods

Coerces a Dna object to a data.frame
Dna-class

Class "Dna" in the Package haplotypes
Parsimnet-class

Class "Parsimnet" in the Package haplotypes
distance-methods

Calculates absolute pairwise character difference matrix using a Dna object
haplotypes-internal

Internal function(s)
as.network-methods

Coerces an object to a network object
dna.obj

Example DNA sequence data
Haplotype-class

Class "Haplotype" in the Package haplotypes
as.numeric-methods

Coerces a Dna object to a numeric matrix
as.networx-methods

Coerces an object to a networx object
as.phyDat-methods

Coerces an object to a phyDat object
as.list-methods

Methods for function as.list in the Package haplotypes
haplotype-methods

Methods for function haplotype in the package haplotypes
boot.dna-methods

Generates single bootstrap replicate