ADMIXTOOLS (or AdmixTools) is a software package that is primarily used for analyzing admixture in
population genetics
Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, s ...
. 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 and OrientAGraph.
Other tools
Related statistical tools in the ADMIXTOOLS software package include qpAdm, qpfst, qpF4ratio, qp3Pop, qpBound, qpDstat, and qpWave. qpDstat and qpWave test whether populations form
clade
In biology, a clade (), also known as a Monophyly, monophyletic group or natural group, is a group of organisms that is composed of a common ancestor and all of its descendants. Clades are the fundamental unit of cladistics, a modern approach t ...
s, while qpAdm estimates ancestry proportions.
is often used in conjunction with
CP/NNLS.
See also
*
SplitsTree
*
Dendroscope
*
List of phylogenetics software
References
External links
AdmixToolsat
GitHub
GitHub () is a Proprietary software, proprietary developer platform that allows developers to create, store, manage, and share their code. It uses Git to provide distributed version control and GitHub itself provides access control, bug trackin ...
AdmixTools 2at
GitHub
GitHub () is a Proprietary software, proprietary developer platform that allows developers to create, store, manage, and share their code. It uses Git to provide distributed version control and GitHub itself provides access control, bug trackin ...
qpGraph software packagein Bioconductor 3.8. {{doi, 10.18129/B9.bioc.qpgraph
admixr– R package for reproducible analyses using ADMIXTOOLS
Phylogenetics software
Free R (programming language) software