The input format of the molecular map should be the same as that of the output format from the program Rmap. The input format of the individual data should be the same as the output format of the program Rcross. If you use an initial genetic model, it should be of the same format as an Rqtl output file. The output of Eqtl will also have such a model, as will the output of MImapqtl itself.
MImapqtl can produce three types of output files. Most results will be put in the qtlcart.mim file, while the Rqtl formatted output file will be qtlcart.mqt. If you choose to calculate residuals, they will be placed in qtlcart.res, which will have the same format as an Rcross output file.