ADMIXTOOLS – tools for admixture testing

The ADMIXTOOLS package implements 5 methods described in Ancient Admixture in Human History by Patterson et al. Genetics (2012).

Details of the methods and algorithm can be found in this paper and in the package’s instructions and examples.

New Version 7.0

Version 7.0 has numerous upgrades.

a) Two new executables –qpfstats qpfmv allow precomputation of f-statistic basis. This can greatly reduce computation costs.

b) qpAdm, qpWave, qpGraph support qpfstats output as input. This is a much improved way of running with allsnps: YES.

c) A new experimental feature of qpGraph (halfscore: YES) allows comparison of 2 phylogenies + a (weak) goodness of fit score. Be careful if running with a large number of populations and consider reducing block size say blgsize: .005

R implementation

Note that several of the new ideas implemented in version 7.0 were developed collaboratively with Robert Maier, who has implemented them along with the great majority of other ADMIXTOOLS functionality in R:

See https://github.com/uqrmaie1/admixtools

Executables run fast, and it has features not available in this C version, such as interactive exploration of graph phylogenies.

A manuscript describing the algorithmic ideas and providing documentation of the methods is in preparation.