pegas

pegas: Population and Evolutionary Genetics Analysis System

pegas is an R package for the analysis of population genetic data.

pegas requires two other R packages: ape and adegenet.

pegas is distributed on CRAN.

The version on CRAN is 0.14 and it can be downloaded here.

The citation for pegas is:

Paradis E. 2010. pegas: an R package for population genetics with an integrated–modular approach.
Bioinformatics 26: 419–420. doi:10.1093/bioinformatics/btp696.

You can find here:

The manual in PDF compiled from the individual help pages: pegas.pdf [272 KB].
A vignette: Reading Genetic Data Files Into R with adegenet and pegas [220 KB].
A document describing the data classes used in pegas: DefinitionDataClassesPegas.pdf [110 KB]

pegas uses data structures from ape to code phylogenies and DNA sequences: details on these structures can be found here.

pegas is also available on GitHub (sometimes with a development version); it can be installed from R with:

library(devtools)
install_github("emmanuelparadis/pegas/pegas")

Updated: September 16, 2020
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