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:	1.4
Depends:	R (≥ 3.2.0), ape (≥ 5.3-11)
Imports:	graphics, utils, methods
Suggests:	rgl, snpStats, adegenet
Published:	2025-12-08
DOI:	10.32614/CRAN.package.pegas
Author:	Emmanuel Paradis [aut, cre, cph], Thibaut Jombart [aut, cph], Zhian N. Kamvar [aut, cph], Brian Knaus [aut, cph], Klaus Schliep [aut, cph], Alastair Potts [aut, cph], David Winter [aut, cph]
Maintainer:	Emmanuel Paradis <Emmanuel.Paradis at ird.fr>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL:	https://emmanuelparadis.github.io/pegas.html
NeedsCompilation:	yes
Citation:	pegas citation info
Materials:	NEWS
CRAN checks:	pegas results

Documentation:

Reference manual:	pegas.html , pegas.pdf
Vignettes:	Plotting Haplotype Networks (source, R code) Reading Files (source, R code)

Downloads:

Package source:	pegas_1.4.tar.gz
Windows binaries:	r-devel: pegas_1.4.zip, r-release: pegas_1.4.zip, r-oldrel: pegas_1.4.zip
macOS binaries:	r-release (arm64): pegas_1.4.tgz, r-oldrel (arm64): pegas_1.4.tgz, r-release (x86_64): pegas_1.4.tgz, r-oldrel (x86_64): pegas_1.4.tgz
Old sources:	pegas archive

Reverse dependencies:

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

Linking:

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