Replaces the traditional criterion by the comparative mapping criterion for a given order data set.
The dsbplambda command is invoked as:
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/rh1_true.cg {1 haploid RH 110 93 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/rh1... CG> dsload Data/order1_ref.cg {2 order 110 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/order1_ref.cg} CG> dsmergor 1 2 {3 merged by order 110 93} #select the comparative mapping criterion CG> dsbplambda 2 1 1 New coefficient factor value is -3.356208. 1.0 #find a first good map CG> lkh 1 -1 [-1015.90] Best map with log10-likelihood = -1015.90 TSP: optimum= 954.887000 lowerbound= 954.107400 gap= 0.081710% totaltime= 0.02 Map -1 : log10-likelihood = -1015.90 -------: Set : Marker List ... 1 : UniSTS158779 UniSTS164109 UniSTS158781 UniSTS158776 UniSTS207126 Uni... 2 : UniSTS158779 UniSTS164109 UniSTS158781 UniSTS158776 UniSTS207126 Uni... #try to improve this map (could be very slow depending on the last paramete... CG> greedy 1 0 5 10 5 Map -1 : log10-likelihood = -1015.90 -------: Set : Marker List ... 1 : UniSTS158779 UniSTS164109 UniSTS158781 UniSTS158776 UniSTS207126 Uni... 2 : UniSTS158779 UniSTS164109 UniSTS158781 UniSTS158776 UniSTS207126 Uni... Run number 0 ------ [-1015.34] [-1015.00] [-1014.44] [-1013.91]-----------------------------------------------------------------... #show the best map in the heap CG> bestprint Map 13 : log10-likelihood = -1013.91 -------: Set : Marker List ... 1 : UniSTS158781 UniSTS164109 UniSTS158779 UniSTS158776 UniSTS207126 Uni... 2 : UniSTS158781 UniSTS164109 UniSTS158779 UniSTS158776 UniSTS207126 Uni... 13 CG>
The description of how to build a reference order dataset in the 'Formatting the data' section.
Thomas Schiex 2018-03-23