Package: haplotypes
Type: Package
Title: Manipulating DNA Sequences and Estimating Unambiguous Haplotype
        Network with Statistical Parsimony
Version: 1.1.3.2
Authors@R: c(person(given = "Caner", family = "Aktas", email = "caktas.aca@gmail.com",role = c("aut", "cre")))
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.  
License: GPL-2
URL: https://cran.r-project.org/package=haplotypes,
        https://biolsystematics.wordpress.com/r/
Depends: R (>= 4.1.0)
Imports: methods, stats, utils, network, sna, ape, phangorn,plotrix
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2025-10-05 16:48:26 UTC; cnr
Author: Caner Aktas [aut, cre]
Maintainer: Caner Aktas <caktas.aca@gmail.com>
Repository: CRAN
Date/Publication: 2025-10-06 07:50:02 UTC
Built: R 4.6.0; ; 2026-04-26 07:59:11 UTC; unix
