Population and Evolutionary Genetics Analysis System R package pegas version 1.4 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. Software Depends: R (>= 3.2.0), ape (>= 5.3-11) Imports: graphics, utils, methods Suggests: rgl, snpStats, adegenet Emmanuel Paradis <Emmanuel.Paradis@ird.fr> Comprehensive R Archive Network (CRAN) Emmanuel Paradis [aut, cre, cph] (ORCID: <https://orcid.org/0000-0003-3092-2199>), Thibaut Jombart [aut, cph] (ORCID: <https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cph] (ORCID: <https://orcid.org/0000-0003-1458-7108>), Brian Knaus [aut, cph] (ORCID: <https://orcid.org/0000-0003-1665-4343>), Klaus Schliep [aut, cph] (ORCID: <https://orcid.org/0000-0003-2941-0161>), Alastair Potts [aut, cph] (ORCID: <https://orcid.org/0000-0003-0919-7279>), David Winter [aut, cph] (ORCID: <https://orcid.org/0000-0002-6165-0029>) GPL (>= 2) 2025-12-08 application/tgz https://CRAN.R-project.org/package=pegas doi:10.32614/CRAN.package.pegas