**Subsections**

##

`lkhd`

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

The `lkhd` command is invoked as either one of :

`lkhd` *Options*
`lkhd` *NbRun* *CollectMaps*

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`).

*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.

nothing.

CG> dsload Data/rh.cg
{1 haploid RH 53 118 /homes/thomas/carthagene/test/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= 0.05
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>

Thomas Schiex
2009-10-27