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

Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel coding methods (only simple indel coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and collapses 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.

Imports: methods, stats, utils, network, sna, ape, phangorn, plotrix
Published: 2023-07-15
DOI: 10.32614/CRAN.package.haplotypes
Author: Caner Aktas
Maintainer: Caner Aktas <caktas.aca at gmail.com>
License: GPL-2
URL: https://cran.r-project.org, https://biolsystematics.wordpress.com/r/
NeedsCompilation: no
Materials: README
CRAN checks: haplotypes results


Reference manual: haplotypes.pdf


Package source: haplotypes_1.1.3.1.tar.gz
Windows binaries: r-devel: haplotypes_1.1.3.1.zip, r-release: haplotypes_1.1.3.1.zip, r-oldrel: haplotypes_1.1.3.1.zip
macOS binaries: r-release (arm64): haplotypes_1.1.3.1.tgz, r-oldrel (arm64): haplotypes_1.1.3.1.tgz, r-release (x86_64): haplotypes_1.1.3.1.tgz, r-oldrel (x86_64): haplotypes_1.1.3.1.tgz
Old sources: haplotypes archive

Reverse dependencies:

Reverse suggests: RAINBOWR


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