If MImapqtl is invoked and an initial model is provided, it will do the following seven steps:
Read in the initial model and convert it to a usable format. The model is read from the file specified by the -E option and must exist.
Estimate all parameters in the initial model. If used, then the initial model simply specifies the positions of the QTL.
Refine the estimates of the positions of all QTL in the initial model. This refinement occurs in the interval where the QTL resides. This is not an option to search other intervals for QTL.
Test each parameter in the initial model for significance. This follows a backward elimination procedure, and those parameters that do not lead to a significant improvement in fit are dropped. The threshold for dropping parameters is specified by the -L option. The information criterion is calculated for the model with and without the tested parameter, and the difference must be greater than the threshold for the effect to be retained.
Search for more QTL. This follows a forward stepwise procedure, whereby the genome is scanned, the most likely place for a new QTL is determined, and if it results in a significant improvement, is retained.
Search for epistatic interactions between the QTL in the model. This will do all pairwise combinations of the QTL that survive steps 4 and 5.
Calculate breeding values, the Variance-Covariance matrix and R2 values for the parameters.
If the user specifies that no initial model is to be used, then the analysis starts with step 5 above.