CMap LPmerge

LPmerge ⁽¹⁾ is a software to create a synthetic consensus map by minimizing the mean absolute error between intervals in the linkage maps and the corresponding intervals in the consensus map. This minimization is performed subject to the constraint that the ordering of the markers in the linkage maps is preserved, which is amenable to linear programming.
When marker order is not consistent across the linkage maps, a minimum set of ordinal constraints is deleted to resolve the conflicts.

The user chooses a reference species/pedigree, the homologous linkage groups in other species/pedigrees that he wishes to analyze. Several species/pedigrees can be analyzed simultaneously. The composite map is performed by comparing the orthologous markers between linkage groups (on the basis of their name). It is therefore necessary to ensure that the sequence homology between markers and rename them accordingly.

The analysis is performed by taking a variable number of "maximum interval size", ranging from 1 to 8 and to estimate the distance on the composite map.
The user indicates linkage groups that he wants to merge and LPmerge returns:

• A graph of "Root Mean Square Error" (RMSE) that indicates errors between the scheduling of the markers in the composite map and individual maps.
• A text file for each estimate of map composite, according to the maximum interval size taken for analysis (8 files, one by interval in the analysis)
• A file containing markers that are a problem (scheduling conflict) in the estimation of the composite map.

From the graph of "Root Mean Square Error", the user can choose the best estimated composite map with the maximum interval size taken in the analysis (the more the mistake made between individual maps is reduced, the less the error made on the composite will be important). The user then selects the output file of the corresponding composite. However, if the RMSE graph is not suitable to the user (too much errors from an individual map on the estimation of the composite, for example), it can return to its analysis, eliminating individual maps which did unsuitable (by unselecting the map). The user will see the conflict markers in the scheduling of markers on the composite map but can not modify in individual maps to remove them.