Hi Ahmed, to calculate the distance between markers you would need a genetic map. To make one you might cross two individuals which are polymorphic in the markers and count the co-occurrences of markers in their offspring - research 'genetic mapping' and 'genetic linkage map' to find out more. What is your species of interest?

Faba bean

At least you may be able to grow a few hundred individuals to make a linkage map then, it is more difficult with animals! You might also find a published map and estimate cM distances if you can locate your markers on this map.

If these markers have been used on F2, DH, RIL, NIL population along with parents you can easily calculate genetic distance using Join Map, Map Maker or Tassel Softwares

You can use Join Map of Map Maker to construct a genetic linkage map with the markers you have which will give the mapping distance in cM

Thank you very much

Join Map, Map maker