Setting rules can be very useful for returning a map order result in a timely matter, especially when you are working with linkage groups that contain a large number of markers or that are complex due to constraints with a framework map. Because finding the optimal marker order can be computationally demanding (depending on the available memory and processing resources), these analyses can take excessive amounts of time or can overwhelm computing resources. These rules enable you to stop the algorithm earlier within a time period and a percentage range of the optimal marker order solution.
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