Tries to optimize the maximum multipoint loglikelihood using a dedicated simulated annealing stochastic optimization algorithm.
The annealing command is invoked either as:
During the search, the algorithm gives some feedback by printing the current temperature and a character ``+'' if an imporved map has been found.
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. # we first load a dataset CG> dsload Data/rh.cg {1 haploid RH 53 118 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/rh.cg} # perform linkage group detection (output omitted) CG> group 0.3 3 ... # select group number 10 CG> mrkselset [groupget 10] # put a (stupid) map in the heap CG> sem Map -1 : log10-likelihood = -161.87 -------: Set : Marker List ... 1 : G5 G18 G17 G14 G16 G13 G12 G6 G7 # use a (fast) annealing command CG> annealing 100 100 0.1 0.9 Map -1 : log10-likelihood = -161.87 -------: Set : Marker List ... 1 : G5 G18 G17 G14 G16 G13 G12 G6 G7 Temp: 100.00 : +++ Temp: 90.00 : Temp: 81.00 : + Temp: 72.90 : Temp: 65.61 : Temp: 59.05 : + Temp: 53.14 : Temp: 47.83 : Temp: 43.05 : Temp: 38.74 : Temp: 34.87 : Temp: 31.38 : Temp: 28.24 : Temp: 25.42 : Temp: 22.88 : Temp: 20.59 : Temp: 18.53 : Temp: 16.68 : Temp: 15.01 : Temp: 13.51 : Temp: 12.16 : Temp: 10.94 : Temp: 9.85 : Temp: 8.86 : Temp: 7.98 : Temp: 7.18 : Temp: 6.46 : Temp: 5.81 : Temp: 5.23 : Temp: 4.71 : Temp: 4.24 : Temp: 3.82 : Temp: 3.43 : Temp: 3.09 : Temp: 2.78 : + Temp: 2.50 : Temp: 2.25 : Temp: 2.03 : Temp: 1.82 : Temp: 1.64 : Temp: 1.48 : Temp: 1.33 : Temp: 1.20 : Temp: 1.08 : Temp: 0.97 : Temp: 0.87 : Temp: 0.79 : Temp: 0.71 : Temp: 0.64 : Temp: 0.57 : Temp: 0.52 : Temp: 0.46 : # we check the map with a large flip CG> flips 9 0 0 Single Flip(window size : 9, threshold : 0.00). Map -1 : log10-likelihood = -141.81 -------: Set : Marker List ... 1 : G7 G12 G13 G16 G6 G5 G17 G18 G14 2 2 2 3 2 1 3 3 2 log10 1 6 7 0 0 9 1 2 8 -141.81 [8 7 6 5 - 3 2 1 0] 0.00 # the map found was indeed optimal
Thomas Schiex 2018-03-23