% MImapqtl -I smprtSeC
Calculates the best model for the dataset in qtlcart.cro using the map in qtlcart.map and the model in qtlcart.eqt, but only searches for main effects (additive and dominance).
Here is a sequence using the example dataset mletest.cro along with its map file mletest.map, both of which come with the programs. Assume that these two files have been placed in an empty subdirectory which is now the current working directory.
% MImapqtl -A -V -I smprtSeC -L 0.0 -S 1 -p 1 -X mletest & % MImapqtl -A -V -I sMPrTseC & % MImapqtl -A -V -I sMPRtseC & % MImapqtl -A -V -I sMPrtSeC & % MImapqtl -A -V -I sMPrtsBC &
The first invocation sets the filename stem, the information criterion and threshold for adding parameters and indicates that it is phase 1. The -I option tells MImapqtl to search for additive QTL. The second invocation tests each QTL found in the first phase. The third step refines the positions of all remaining QTL. The fourth step searches for more QTL (and probably won't find any). The fifth step searches for interactions between the identified putative QTL. The phase variable is updated after each step, so MImapqtl knows where to find the results from the previous step.