nicemapl

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

Synopsis:

The nicemapl command is invoked as either one of :

• nicemapl Options
• nicemapl

Description:

The nicemapl 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 marker with the strongest LOD as the next 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 be used preferably to nicemapd when some data-sets have been merged with separate parameter 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> nicemapl

Map -1 : log10-likelihood =  -344.26
-------:
 Set : Marker List ...
   1 : MS14 MS13 MS11 MS10 MS5 MS6 MS1 MS2 MS3 MS4 MS7 MS8 MS9 MS12 MS15 MS16\
 MS17 MS18 MS19 MS20

See also:

• sem (2.5.2)
• nicemapd (2.5.6)
• mfmapl (2.5.7)
• mfmapd (2.5.8)
• build (2.5.17)
• buildfw (2.5.19)