We will introduce a simple approach. In practice you have to choose among the approaches that fits the situation the best. It is just a preference or choice of approaches to reduce the number of unnecessary runs before you reach the optimium marker order. To find out possible unfit marker orders in an existing marker order array , use option flip . The last field of the results shows the difference of the likelihoods between the original and the flipped orders of two adjecent markers, therefore we want it to be positive.
Any negative value indicates that the flipped order is better.
By repeating the flip and all options, you will get the best order. NOTE that there are more options in crimap analysis that we have not covered here. For example, Option chrompic is extremely useful in checking genotype data for potential errors and conflicting results among markers. Option build is useful in gradually building up a map by adding markers one at a time. It is useful when build a map de novo.