poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data

Functions for the computation of f- and D-statistics (estimation of 'Fst', Patterson's 'F2', 'F3', 'F3*', 'F4' and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as 'vcf' files or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in 'TreeMix', 'BayPass' or 'SelEstim' format).

Version:	2.2.0
Depends:	R (≥ 3.0)
Imports:	Rcpp (≥ 1.0.5), methods, data.table, utils, foreach, doParallel, parallel, DiagrammeR, ape, stats, zoo, Ryacas, Matrix, RcppProgress, progress, nnls
LinkingTo:	Rcpp, RcppProgress
Published:	2023-09-06
Author:	Mathieu Gautier
Maintainer:	Mathieu Gautier <mathieu.gautier at inrae.fr>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	yes
Citation:	poolfstat citation info
Materials:	ChangeLog
CRAN checks:	poolfstat results

Documentation:

Reference manual:	poolfstat.pdf
Vignettes:	poolfstatvignette

Downloads:

Package source:	poolfstat_2.2.0.tar.gz
Windows binaries:	r-devel: poolfstat_2.2.0.zip, r-release: poolfstat_2.2.0.zip, r-oldrel: poolfstat_2.2.0.zip
macOS binaries:	r-release (arm64): poolfstat_2.2.0.tgz, r-oldrel (arm64): poolfstat_2.2.0.tgz, r-release (x86_64): poolfstat_2.2.0.tgz, r-oldrel (x86_64): poolfstat_2.2.0.tgz
Old sources:	poolfstat archive

Linking:

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