tess3r is an R package for estimating and visualizing spatial population structure based on geographically constrained non-negative matrix factorization and population genetics. tess3r has fast and efficient algorithms for estimating ancestry coefficients and for running genome scans for selection (see Overview).
Install the latest version from github (requires devtools):
# install.packages("devtools")
devtools::install_github("bcm-uga/TESS3_encho_sen")-
Kevin Caye, Timo Deist, Helena Martins, Olivier Michel, Olivier Francois (2016) TESS3: fast inference of spatial population structure and genome scans for selection. Molecular Ecology Resources 16 (2), 540-548. doi: 10.1111/1755-0998.12471.
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Kevin Caye, Flora Jay, Olivier Michel, Olivier Francois. Fast Inference of Individual Admixture Coefficients Using Geographic Data. bioRxiv, 2016, doi: http://dx.doi.org/10.1101/080291
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Helena Martins, Kevin Caye, Keurcien Luu, Michael GB Blum, Olivier Francois (2016). Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics. Molecular Ecology 25 (20), 5029-5042. doi: http://dx.doi.org/10.1101/054585.
