Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
Version: | 1.0 |
Depends: | R (≥ 3.2.0), ape (≥ 5.3-11) |
Imports: | graphics, utils, methods, adegenet |
Suggests: | rgl, snpStats |
Published: | 2021-04-08 |
Author: | Emmanuel Paradis |
Maintainer: | Emmanuel Paradis <Emmanuel.Paradis at ird.fr> |
License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
URL: | http://ape-package.ird.fr/pegas.html |
NeedsCompilation: | yes |
Citation: | pegas citation info |
Materials: | NEWS |
In views: | Phylogenetics |
CRAN checks: | pegas results |
Reference manual: | pegas.pdf |
Vignettes: |
Plotting Haplotype Networks Reading Files |
Package source: | pegas_1.0.tar.gz |
Windows binaries: | r-devel: pegas_1.0.zip, r-devel-UCRT: pegas_1.0.zip, r-release: pegas_1.0.zip, r-oldrel: pegas_0.14.zip |
macOS binaries: | r-release: pegas_1.0.tgz, r-oldrel: pegas_0.14.tgz |
Old sources: | pegas archive |
Reverse depends: | adhoc, StAMPP |
Reverse imports: | graph4lg, HACSim, HierDpart, mmod, PopGenReport, poppr, RAINBOWR, spider |
Reverse suggests: | adegenet, dartR, hierfstat, pagoo |
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