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haplotypes
Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony
View on CRAN: Click
here
Download and install haplotypes package within the R console
Install from CRAN:
install.packages("haplotypes")
Install from Github:
library("remotes")
install_github("cran/haplotypes") Install by package version:
library("remotes")
install_version("haplotypes", "1.1.3.1") Attach the package and use:
library("haplotypes")
Maintained by
Caner Aktas
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-04-26
Latest Update: 2023-07-15
Description:
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.
How to cite:
Caner Aktas (2015). haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony. R package version 1.1.3.1, https://cran.r-project.org/web/packages/haplotypes. Accessed 02 Feb. 2025.
Previous versions and publish date:
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Complete documentation for haplotypes
Functions, R codes and Examples using
the haplotypes R package
Some associated functions: Dna-class . Haplotype-class . Parsimnet-class . append-methods . as.DNAbin-methods . as.data.frame-methods . as.dna-methods . as.list-methods . as.matrix-methods . as.network-methods . as.networx-methods . as.numeric-methods . as.phyDat-methods . basecomp-methods . boot.dna-methods . distance-methods . dnaj . grouping-methods . haplotype-methods . haplotypes-internal . haplotypes-package . hapreord-methods . homopoly-methods . image-methods . indelcoder-methods . length-methods . names-methods . ncol-methods . nrow-methods . pairPhiST-methods . pairnei-methods . parsimnet-methods . pielegend-methods . pieplot-methods . plot-methods . polymorp-methods . range-methods . read.fas . remove.gaps-methods . rownames-methods . show-methods . subs-methods . tolower-methods . unique-methods . z[-methods .
Some associated R codes: Full haplotypes package functions and examples
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