Like "compare", the "map" command instructs MAPMAKER to calculate the maximum likelihood map of each order specified by the current sequence. If the current sequence specifies more than one order (for example, the sequence "{1 2 3 5 7}" specifies 60 orders) then the maps for all specified orders will be calculated and displayed.
Because we found one order of this group to be much more likely than any other, we probably only care to see the map distances for this single order. First, we set MAPMAKER's sequence, putting the markers in their best order and doing away with the set brackets.
Next, we simply type "map" to display this order's maximum likelihood map.
As you can see, the distances between neighboring markers are displayed. Note however, that these distances may be considerably different than the "two-point" distances between those markers: This is because MAPMAKER's so-called multipoint analysis facility can take into account much more information, such as flanking marker genotypes and some amount of missing data. This is precisely the reason that we use multipoint analysis rather than two point analysis to order markers: Because more data is taken into account, you have a smaller chance of making a mistake.
7> sequence 1 3 2 5 7 sequence #3= 1 3 2 5 78> map ===================================================================== Map: Markers Distance 1 T175 4.2 cM 3 C35 15.0 cM 2 T93 11.9 cM 5 C66 12.2 cM 7 T50B ---------- 43.2 cM 5 markers log-likelihood= -424.94 ====================================================================