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: 0.12
Depends: R (≥ 2.6.0), ape (≥ 2.4), adegenet
Imports: graphics, utils, methods
Suggests: rgl, snpStats
Published: 2019-10-05
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 [aut, cph], Alastair Potts ORCID iD [aut, cph], David Winter ORCID iD [aut, cph]
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

Downloads:

Reference manual: pegas.pdf
Vignettes: Reading Files
Package source: pegas_0.12.tar.gz
Windows binaries: r-devel: pegas_0.12.zip, r-devel-gcc8: pegas_0.12.zip, r-release: pegas_0.12.zip, r-oldrel: pegas_0.12.zip
OS X binaries: r-release: pegas_0.12.tgz, r-oldrel: pegas_0.12.tgz
Old sources: pegas archive

Reverse dependencies:

Reverse depends: adhoc, StAMPP
Reverse imports: dartR, graph4lg, HACSim, haplotypes, HierDpart, mmod, PopGenReport, poppr, rmetasim, skeleSim, spider, strataG
Reverse suggests: adegenet, BarcodingR, hierfstat

Linking:

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