pegas

MaRDI QIDQ20317swMATHCRANFDO

Authors 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)

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

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