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 (depends) and adegenet (suggests).

pegas is distributed on CRAN and on GitHub. The version on CRAN is 1.3.

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 vignette: Plotting Haplotype Networks with pegas [300 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.

Updated: December 13, 2023
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