lkhd

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

Synopsis:

The lkhd command is invoked as either one of :

• lkhd Options
• lkhd NbRun CollectMaps

Description:

The lkhd command converts the current marker selection and associated genetic / Radiated Hybrid data into a Traveling Salesman Problem which is solved using Keld Helsgaun's LKH software. LKH is based on the Lin-Kernighan heuristic. It is possible to collect every tour found by LKH into the CarthaGene heap, in order to get a map with a possible better multipoint loglikelihood.

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.
• NbRun : Repeats NbRun times the LK heuristic.
• CollectMaps : Possible values are -1, 0, 2, 3, 4 and 5. If CollectMaps >= 0 then every tour found by LKH is inserted into the CarthaGene heap. Moreover, a positive value sets the backtrack move type of LKH.

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/rh.cg
{1 haploid RH 53 118 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/rh.cg}
CG> lkhd 1 -1
[-833.04]
Best map with log10-likelihood = -833.04
TSP: optimum= 16.678000 lowerbound= 16.676800 gap= 0.007196% totaltime= 0.01

Map -1 : log10-likelihood =  -833.04
-------:
 Set : Marker List ...
   1 : MS1 G39 MS3 MS2 G37 G40 G36 MS4 G1 MS5 G4 G3 G2 MS6 MS7 MS9 MS8 G21 G2\
6 G22 G25 G23 G27 G24 G28 G34 G33 G30 G29 G31 G32 G35 MS13 G5 G17 G14 MS15 G1\
5 G18 G16 G6 G13 G12 G7 G8 G11 G20 MS17 G19 MS19 G9 G10 MS20

CG>

See also:

• lkh (2.5.9)
• lkhn (2.5.10)
• lkhl (2.5.11)
• cg2tsp (2.5.15)