lkhocbn

Computes an intuitively nice marker ordering using normalized 2-points Obligate Chromosome Breaks criterion.

Synopsis:

The lkhocbn command is invoked as either one of :

• lkhocbn Options
• lkhocbn NbRun CollectMaps

Description:

The lkhocbn 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.

Returns:

nothing.

Example:

CG> dsload Data/rh.cg
{1 haploid RH 53 118 /homes/thomas/carthagene/test/Data/rh.cg}
CG> lkhocbn 1 -1
[-823.85]
Best map with log10-likelihood = -823.85
TSP: optimum= 627.818000 lowerbound= 627.582000 gap= 0.037605% totaltime= 0.09

Map -1 : log10-likelihood =  -823.85
-------:
 Set : Marker List ...
   1 : MS17 G20 G19 MS19 G9 G10 G11 G8 G7 G12 G13 G16 G6 G5 G17 G18 G14 G15 M\
S15 G35 MS13 G32 G29 G31 G30 G33 G34 G28 G24 G27 G23 G25 G22 G26 G21 MS8 MS9 \
MS7 MS6 G2 G1 MS5 G4 G3 MS4 G36 G40 G37 MS2 MS3 G39 MS1 MS20

CG>

See also:

• lkhocb (2.5.12)
• lkh (2.5.8)
• cg2tsp (2.5.14)