# LM_LODS:

input pedigree file 'ped45'
output seed file 'seed15'
input seed file 'seed15'
output score file '/dev/null'

select chrom 2 markers 5  traits 1

map chrom 2  gender F  markers            recomb fract .2 .2 .2 .2 
map chrom 2  gender M  markers            recomb fract .2 .2 .2 .2 

set chromosome 2  markers 1 2 3 4 5   freqs  .2 .2 .4 .2
set trait   1             freqs  .95 .05

map chrom 2 trait 1 interval proportions .2 .5 .8
map chrom 2 trait 1 external recomb fracts  .05 .15 .25 .35 .45

set chromosome 2 marker data
  333   1 3  1 3  1 3  1 3  1 3 
  331   3 4  3 4  3 4  3 4  3 4 
  334   2 3  2 3  2 3  2 3  2 3 
  431   3 4  3 4  3 4  3 4  3 4 
  531   3 3  3 3  3 3  3 3  3 3 

set L-sampler probability 0.2 

set MC iterations 2000

output scores 10000 MC iterations