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:

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>

See also:

• lkh (2.5.8)
• lkhn (2.5.9)
• lkhl (2.5.10)
• cg2tsp (2.5.14)