sNMF

sNMF is an R tool to estimate individual admixture coefficients. The sNMF algorithm uses sparse non-negative matrix factorization and population genetics. According to the Authors, sNMF is about 10 to 30 times faster than ADMIXTURE.

Topic

Population genetics

Detail

Operation: Genetic variation analysis
Software interface: Command-line user interface
Language: R
License: GNU General Public License v3
Cost: Free
Version name: 2.0
Credit: la Région Rhône-Alpes, Grenoble Institute of Technology.
Input: -
Output: -
Contact: Eric Frichot: eric.frichot@gmail.com, eric.frichot@imag.fr, Olivier François: olivier.francois@grenoble-inp.fr
Collection: -
Maturity: Stable

Publications

Fast and efficient estimation of individual ancestry coefficients.
Frichot E, Mathieu F, Trouillon T, Bouchard G, François O. Fast and efficient estimation of individual ancestry coefficients. Genetics. 2014 Apr;196(4):973-83.
https://doi.org/10.1534/genetics.113.160572
PMID: 24496008
PMC: PMC3982712

Download and documentation

Source: http://membres-timc.imag.fr/Olivier.Francois/snmf/files/sNMF_CL_v1.2.zip
Documentation: http://membres-timc.imag.fr/Olivier.Francois/LEA/tutorial.htm
Home page: http://membres-timc.imag.fr/Olivier.Francois/snmf/index.htm
Links: http://membres-timc.imag.fr/Olivier.Francois/LEA/faq.htm

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