pegas: Population and Evolutionary Genetics Analysis System

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: 1.3
Depends: R (≥ 3.2.0), ape (≥ 5.3-11)
Imports: graphics, utils, methods
Suggests: rgl, snpStats, adegenet
Published: 2023-12-13
DOI: 10.32614/CRAN.package.pegas
Author: Emmanuel Paradis ORCID iD [aut, cre, cph], Thibaut Jombart ORCID iD [aut, cph], Zhian N. Kamvar ORCID iD [aut, cph], Brian Knaus ORCID iD [aut, cph], Klaus Schliep ORCID iD [aut, cph], Alastair Potts ORCID iD [aut, cph], David Winter ORCID iD [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: pegas citation info
Materials: NEWS
CRAN checks: pegas results


Reference manual: pegas.pdf
Vignettes: Plotting Haplotype Networks
Reading Files


Package source: pegas_1.3.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): pegas_1.3.tgz, r-oldrel (arm64): pegas_1.3.tgz, r-release (x86_64): pegas_1.3.tgz, r-oldrel (x86_64): pegas_1.3.tgz
Old sources: pegas archive

Reverse dependencies:

Reverse depends: StAMPP
Reverse imports: geneHapR, graph4lg, HACSim, mmod, PopGenReport, poppr, RAINBOWR, spider, wingen
Reverse suggests: adegenet, dartR, dartR.base, hierfstat


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