This is a Julia file for genomic optimum contribution and mate allocation using JuMP. The genomic markers are available in QTLMAS2010gen.zip, and the true breeding values and gender indicators are in tbv.txt. You need to install the following Julia packages: DelimitedFiles, Statistics, JuMP, LinearAlgebra, COSMO, Plots and SCIP.
Please see the paper: Waldmann, P. (2025). Genomic Optimum Contribution Selection and Mate Allocation Using JuMP. Bioinformatics Advances: https://doi.org/10.1093/bioadv/vbaf259

The file GBLUPAIREML.jl performs standard GBLUP based on the classic Average Information Restricted Maximum Likelihood (AIREML) algorithm. The code needs a phenotype file (a column vector), a marker file with SNPs (coded 0, 1 or 2) in columns without missing data, a fixed effect file (minimum is a vector of ones for the mean) and a separate random effects file (can be empty if there are no extra random effects). The code allows for missing data (NA) in the phenotype. You need to specify the names of the output files at the end of the code.