Abstract: Disclosed is a computer-implemented method of determining at least one optimal alignment of at least part of a first map to at least part of a second map or a plurality of second maps, wherein the maps are physical genome maps and/or restriction maps. The method comprises: receiving first map data indicative of a first ordered list of distances between features of the first map, receiving second map data indicative of a second ordered list of distances between features of the second map or second maps; generating, from the second map data, seed data indicative of a plurality of seeds, each seed comprising at least one of the distances in the second ordered list, wherein the features are restriction sites and distances are fragment sizes.