pegas

swMATH8307CRANpegasMaRDI QIDQ20317FDOQ20317

Population and Evolutionary Genetics Analysis System

Zhian N. Kamvar, Klaus Schliep, Emmanuel Paradis, Brian J. Knaus, Thibaut Jombart, David J. Winter, Alastair J. Potts

Last update: 13 December 2023

Copyright license: GNU General Public License, version 3.0, GNU General Public License, version 2.0

Software version identifier: 1.2, 0.1, 0.2, 0.3-1, 0.3-2, 0.3-3, 0.3-4, 0.3, 0.4-1, 0.4-2, 0.4-3, 0.4-4, 0.4-5, 0.4, 0.5-1, 0.5, 0.6, 0.7, 0.8-1, 0.8-2, 0.8, 0.9, 0.10, 0.11, 0.12, 0.13, 0.14, 1.0-1, 1.0, 1.1, 1.3

Official website: http://cran.r-project.org/web/packages/pegas/index.html

Source code repository: https://github.com/cran/pegas

Description

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.

Cited In (18)

• Clustal
• LASER
• SeqinR
• rehh
• snpQC
• ZEUS-3D
• Pegas
• mmod
• Primer to analysis of genomic data using R
• StAMPP
• poppr
• geneHapR
• graph4lg
• Analysis of phylogenetics and evolution with R
• Using the PPML approach for constructing a low-dissipation, operator-splitting scheme for numerical simulations of hydrodynamic flows
• HACSim
• RAINBOWR
• spider

This page was built for software: pegas