sample.inp

remark  Define two chromosomes, arbitrarily named "one" and "two"
make chromosome one two

remark  Chromosome one will be the linkage group which contains marker 1
remark  Chromosome two will be the linkage group which contains marker 4
sequence 1 
anchor one
sequence 4
anchor two

remark  Now we assign all of the markers to one of these two chromosomes. We
remark  need to do this in order to make frameworks, as the framework for a
remark  chromosome must only contain markers assigned to that chromosome...
sequence all
assign

remark  Now we finally can set the framework maps for the two chromosomes...
sequence 1 3 2 5 7
frame one
sequence 4 11 8 12 9 6 10
frame two