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eigensoft
The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations.
FigTree
FigTree is designed as a graphical viewer of phylogenetic trees.
fbat
FBAT implements a broad class of Family Based Association Tests, adjusted for population admixture.
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