Subsections

## lkhn

Computes an intuitively nice marker ordering using normalized 2-points loglikelihoods.

#### Synopsis:

The lkhn command is invoked as either one of :

• lkhn Options
• lkhn NbRun CollectMaps

#### Description:

The lkhn 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.

#### 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.

nothing.

#### Example:

```CG> dsload Data/rh.cg
{1 haploid RH 53 118 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/rh.cg}
CG> lkhn 1 -1
[-823.30]
Best map with log10-likelihood = -823.30
TSP: optimum= 822.235000 lowerbound= 822.222200 gap= 0.001557% totaltime= 0.10

Map -1 : log10-likelihood =  -823.30
-------:
Set : Marker List ...
1 : MS1 G39 MS3 MS2 G37 G40 G36 MS4 G3 G4 MS5 G1 G2 MS6 MS7 MS9 MS8 G21 G2\
6 G22 G25 G23 G27 G24 G28 G34 G33 G30 G31 G29 G32 G35 MS13 MS20 MS17 G20 G19 \
MS19 G9 G10 G11 G8 G7 G12 G13 G16 G6 G5 G17 G18 G14 MS15 G15

CG>
```