MImapqtl can read a genetic model and proced with various tasks as explained above. This leads to the idea of repeating the analysis with the results of a previous run of the program. One can think of doing the analysis in steps or phases. The default is to set the phase to zero. If the phase is set to zero, then the default input file for a genetic model is qtlcart.eqt, the output is qtlcart.mqt and the general output file is qtlcart.mim. At the end of the analysis, the phase remains 0.
If one sets the phase to a positive integer (generally starting with 1), then the default input is to assume that input and output files follow a rule. Assume the filename stem is qtlcart and the phase is i. The input genetic model will be set to qtlcartPhasei-1.mqt, the output genetic model will be written to qtlcartPhasei.mqt, and the general output file will be qtlcartPhasei.mim. At the end of the analysis, the phase variable i will be incremented by one and recorded in the qtlcart.rc file. This makes it easier for the program (and the user) to keep track of previous and current results. Also note that if you used an R in position 7 of the workcode, then the output file containing a new dataset with the residuals replacing the trait values will be put in qtlcartPhasei.res.