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 infering 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.

Package details

AuthorCaner Aktas
MaintainerCaner Aktas <[email protected]>
LicenseGPL-2
Version1.1
URL https://cran.r-project.org https://biolsystematics.wordpress.com/r/
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("haplotypes")

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haplotypes documentation built on May 2, 2019, 5:50 a.m.