ADMIXTOOLS

ADMIXTOOLS (or AdmixTools) is a software package that is primarily used for analyzing admixture in population genetics. The original version was developed as a set of standalone C programs by Nick Patterson and colleagues and published in 2012. A reimplemented version, ADMIXTOOLS 2, was developed as an R package by Robert Maier and colleagues and published in 2023.

Most ADMIXTOOLS programs are based on fitting demographic models to f-statistics, which are calculated from population allele frequencies.

qpGraph
qpGraph is a software program that is part of the ADMIXTOOLS software package developed by Patterson et al. (2012). qpGraph evaluates graph-based models of population relationships with genetic admixture. It estimates likelihoods of graphs with a fixed topology, while adjusting graph parameters to fit observed f-statistics.

ADMIXTOOLS 2 adds functionality for finding optimized graph topologies, similar to programs like Treemix.

Other tools
Related statistical tools in the ADMIXTOOLS software package include qpAdm, qpDstat, and qpWave. qpDstat and qpWave test whether populations form clades, while qpAdm estimates ancestry proportions. qpAdm is often used in conjunction with CP/NNLS.