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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.
| Version: | 1.1.3.1 |
| 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 suggests: | RAINBOWR |
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