pegas

pegas: Population and Evolutionary Genetics Analysis System

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

pegas is entirely written in R.

pegas requires two other R packages: ape for the functions that analyse DNA data (haplotype, MMD, R2.test, tajima.test), and adegenet for some conversion functions (genind2loci, loci2genind).

pegas is distributed on CRAN.

The version on CRAN is 0.4-1 and its sources can be downloaded here.

You can find here:

The manual in PDF compiled from the individual help pages: pegas.pdf [190 KB].
A vignette: Reading Genetic Data Files Into R with adegenet and pegas [110 KB].
A document describing the data classes used in pegas: DefinitionDataClassesPegas.pdf [56 KB]

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

pegas is still in its early stage of development. Any feedback is welcome.

All materials on this page are coyrighted:
(c) Emmanuel Paradis, 2012 - Last updated: January 19, 2012