mfmapd

Computes an intuitively nice marker ordering using 2-points distances.

Synopsis:

The mfmapd command is invoked as either one of :

• mfmapd Options
• mfmapd

Description:

The mfmapd command builds gradually a map by inserting the best (whose distances are minima) available pairs of markers among the current list of active markers. This ``Greedy'' heuristic applies a multi-fragment (mf) strategy: several order fragments of markers which are close together are constructed and then linked together.

Warning: since 2-points estimations are typically unavailable for some pairs of markers when data-sets are merged, this command will return very poor maps on such merged data. This command should especially not be used when two data-sets have been merged with separate parameters estimation (using mergor).

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.

Example:

   CarthaGene version 1.2-LKH, Copyright (c) 1997-2010 (INRA).

   CarthaGene comes with ABSOLUTELY NO WARRANTY.
   CarthaGene is free software. You are welcome to redistribute it,
   under certain conditions. See the License file for information.

Type 'help' for help.

CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/b...
CG> mfmapd

Map -1 : log10-likelihood =  -321.28
-------:
 Set : Marker List ...
   1 : MS1 MS2 MS3 MS4 MS5 MS7 MS6 MS8 MS11 MS10 MS9 MS14 MS12 MS13 MS16 MS15\
 MS17 MS18 MS19 MS20

See also:

• mfmapl (2.5.7)
• nicemapd (2.5.6)
• nicemapl (2.5.5)
• sem (2.5.2)