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).


Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.


2.0.0 by Mathieu Gautier, 8 months ago

Browse source code at

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