Tries to optimize the maximum multipoint loglikelihood using a dedicated genetic algorithm.
The CarthaGene algogen command is invoked as either one of :
As the algorithm runs, ``+'' are printed on a generation such that a map is found that improves over the best map known.
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 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 ... # we select the group 10 CG> mrkselset [groupget 10] # put one (stupid) map in the heap using the 'sem' command CG> sem Map -1 : log10-likelihood = -161.87 -------: Set : Marker List ... 1 : G5 G18 G17 G14 G16 G13 G12 G6 G7 # launch the 'algogen' command CG> algogen 10 8 1 0.6 0.1 1 + - - - - - - - - - # check the reliability of the result 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 was optimal
Thomas Schiex 2018-03-23