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).


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install.packages("poolfstat")

2.0.0 by Mathieu Gautier, 2 months ago


Browse source code at https://github.com/cran/poolfstat


Authors: Mathieu Gautier


Documentation:   PDF Manual  


GPL (>= 2) license


Imports Rcpp, methods, utils, foreach, doParallel, parallel, DiagrammeR, ape, stats, zoo, Ryacas, Matrix, RcppProgress, progress, nnls

Linking to Rcpp, RcppProgress


See at CRAN