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One special case of G x E analysis has been incorporated into
JZmapqtl, namely the situation where a set of genotypes is raised in more than one environment.
The value of the trait in each environment is treated as a separate trait for the common genotype.
For this type of data, use hypothesis 14 or 34 to invoke the G x E analysis. Hypothesis 14 is for
data with two marker genotypes, while 34 is for three marker genotypes. There will be an extra column
in the output that give a likelihood ratio for a G x E effect versus no effect. When running Eqtl
subsequent to doing a G x E analysis, be sure to specify the same hypothesis test.