The BIMBAM software [22] can be run in two different ways: 1) using option –mph 1, which tests for association between the multivariate traits, all partitioned in the group of directly affected traits, and genotype; and 2) using option –mph2, which considers all the different possible partitions of traits into the different categories of traits (directly affected, indirectly affected, unaffected). We applied option –mph2 under the additive model using the following command: bimbam -g geno.txt -p pheno.txt -o output -f 3 -mph2 -A 0.1 -A 0.2.
