sem

Computes the maximum likelihood of the current active markers order.

Synopsis:

The sem command is invoked either as:

• sem Options
• sem

Description:

The sem command (for ``Single EM'') performs the maximum likelihood estimation of all the needed recombination /breakage/retention ratio parameters for the current data-set using the current marker ordering (available using the mrkselget command). The map obtained is submitted for the heap and is therefore memorized if it is close enough to the optimum map.

Arguments:

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.

Returns:

nothing. The map is submitted to the heap.

Example:

CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /homes/thomas/carthagene/test/Data/bc.cg}
CG> mrkselget
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
CG> sem

Map -1 : log10-likelihood =  -297.78
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS3 MS4 MS5 MS6 MS7 MS8 MS9 MS10 MS11 MS12 MS13 MS14 MS15 MS16\
 MS17 MS18 MS19 MS20

CG>

See also:

• mrkselset (2.3.14)