Several scripts that I have built and am now making available.
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Script to estimate the relationship matrix using SNP data: Additive from VanRaden (2008) and dominance matrix from Vitezica (2013) and Su et al. (2012).
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Inbreeding measure from the SNP dataset.
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Quadpop example. I'll try to incorporate it later.
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Dominated Pareto implementation. It works just fine for a few thousand data points.
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Simulation via AlphaSimR of a breeding program using BGLR and multi-traits.