nicemapd

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

Synopsis:

The nicemapd command is invoked as either one of :

• nicemapd Options
• nicemapd

Description:

The nicemapd command orders the current list of active markers using a simple Nearest Neighbor heuristics. Starting from each marker successively, it builds a map by always selecting the nearest marker. The best map according to multipoint maximum likelihood is inserted in the heap.

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> nicemapd

Map -1 : log10-likelihood =  -325.47
-------:
 Set : Marker List ...
   1 : MS13 MS14 MS11 MS10 MS9 MS8 MS7 MS6 MS5 MS4 MS3 MS2 MS1 MS12 MS15 MS16\
 MS18 MS17 MS19 MS20

See also:

• nicemapl (2.5.5)
• mfmapd (2.5.8)
• mfmapl (2.5.7)
• sem (2.5.2)