Precisely describes the best map in the current Pareto frontier.
The paretobestprintd 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} #speed up likelihood computation (2-point mode) CG> cg2pt 1 #build a Pareto frontier from scratch CG> paretolkh 10 1 0 ... #restore multipoint likelihood computation CG> cg2pt 0 #recompute multipoint likelihood estimates for every map in the heap CG> cgtolerance 0.0009 0.09 #improve the Pareto frontier only near the current best map CG> paretogreedyr 25 4 8 ... #show the best map in the improved frontier, in details CG> paretobestprintd 1 Pareto frontier approximation (coverage: 34 / 35 = 97.14 %): Ranges: Log10-likelihood [-1012.378,-963.611] / BP [3,37] = 1.4343 Id: 69 BP: 37 Log10-like: -963.611 Log10-like+bp: -1087.232 Id: 65 BP: 36 Log10-like: -963.611 Log10-like+bp: -1083.645 Id: 59 BP: 35 Log10-like: -963.682 Log10-like+bp: -1080.127 do... Id: 63 BP: 34 Log10-like: -963.611 Log10-like+bp: -1076.466 Id: 57 BP: 33 Log10-like: -963.682 Log10-like+bp: -1072.946 do... Id: 61 BP: 32 Log10-like: -963.681 Log10-like+bp: -1069.354 Id: 53 BP: 31 Log10-like: -964.707 Log10-like+bp: -1066.788 do... Id: 55 BP: 30 Log10-like: -964.706 Log10-like+bp: -1063.197 Id: 49 BP: 29 Log10-like: -965.007 Log10-like+bp: -1059.909 do... Id: 51 BP: 28 Log10-like: -965.007 Log10-like+bp: -1056.320 Id: 47 BP: 27 Log10-like: -966.928 Log10-like+bp: -1054.655 Id: 83 BP: 25 Log10-like: -968.604 Log10-like+bp: -1049.165 do... Id: 45 BP: 24 Log10-like: -966.968 Log10-like+bp: -1043.952 Id: 87 BP: 23 Log10-like: -968.115 Log10-like+bp: -1041.525 Id: 79 BP: 22 Log10-like: -970.281 Log10-like+bp: -1040.122 Id: 73 BP: 21 Log10-like: -971.429 Log10-like+bp: -1037.706 do... Id: 75 BP: 20 Log10-like: -970.496 Log10-like+bp: -1033.215 Id: 68 BP: 19 Log10-like: -971.716 Log10-like+bp: -1030.884 Id: 60 BP: 18 Log10-like: -973.812 Log10-like+bp: -1029.437 do... Id: 64 BP: 17 Log10-like: -972.866 Log10-like+bp: -1024.955 Id: 52 BP: 16 Log10-like: -978.995 Log10-like+bp: -1027.557 do... Id: 56 BP: 15 Log10-like: -977.722 Log10-like+bp: -1022.766 Id: 48 BP: 14 Log10-like: -979.440 Log10-like+bp: -1020.977 Id: 44 BP: 13 Log10-like: -982.586 Log10-like+bp: -1020.628 Id: 81 BP: 12 Log10-like: -984.293 Log10-like+bp: -1018.852 Id: 72 BP: 11 Log10-like: -986.058 Log10-like+bp: -1017.145 Id: 88 BP: 10 Log10-like: -988.552 Log10-like+bp: -1016.182 Id: 80 BP: 9 Log10-like: -991.197 Log10-like+bp: -1015.382 Id: 78 BP: 8 Log10-like: -993.404 Log10-like+bp: -1014.158 Id: 37 BP: 7 Log10-like: -996.049 Log10-like+bp: -1013.383 **... Id: 38 BP: 6 Log10-like: -999.751 Log10-like+bp: -1013.673 Id: 50 BP: 5 Log10-like: -1003.668 Log10-like+bp: -1014.173 Id: 16 BP: 4 Log10-like: -1008.346 Log10-like+bp: -1015.405 Id: 19 BP: 3 Log10-like: -1012.378 Log10-like+bp: -1015.873 Map 37 : log10-likelihood = -996.05, log-e-likelihood = -2293.49 -------: Data Set Number 1 : Markers Distance Cumulative Theta 2pt Pos Id name (%%age) LOD 1 4 UniSTS158779 5.3 cR 0.0 cR 5.2 % 20.9 2 5 UniSTS164109 8.6 cR 5.3 cR 8.2 % 18.4 3 6 UniSTS158781 85.9 cR 13.9 cR 57.6 % 3.8 4 3 UniSTS158776 17.8 cR 99.8 cR 16.3 % 15.1 5 2 UniSTS207126 11.6 cR 117.5 cR 11.0 % 17.5 6 1 UniSTS178358 114.8 cR 129.1 cR 68.3 % 2.2 7 110 UniSTS158909 28.8 cR 243.9 cR 25.0 % 11.3 8 109 UniSTS178555 11.8 cR 272.7 cR 11.1 % 15.9 9 108 UniSTS165135 11.8 cR 284.5 cR 11.1 % 15.5 10 107 UniSTS158905 0.0 cR 296.3 cR 0.0 % 22.0 11 106 UniSTS158906 8.8 cR 296.3 cR 8.4 % 16.3 12 105 UniSTS178551 30.8 cR 305.1 cR 26.5 % 8.4 13 104 UniSTS185461 26.6 cR 335.9 cR 23.4 % 9.6 14 103 UniSTS165128 8.9 cR 362.5 cR 8.5 % 16.7 15 102 UniSTS178540 30.3 cR 371.3 cR 26.1 % 9.4 16 101 UniSTS178545 42.5 cR 401.6 cR 34.6 % 6.5 17 100 UniSTS158900 0.0 cR 444.1 cR 0.0 % 20.4 18 99 UniSTS164142 27.3 cR 444.1 cR 23.9 % 9.9 19 98 UniSTS185460 14.4 cR 471.4 cR 13.4 % 13.8 20 97 UniSTS178531 10.5 cR 485.8 cR 9.9 % 15.5 21 96 UniSTS178530 74.4 cR 496.2 cR 52.5 % 3.8 22 95 UniSTS178523 26.4 cR 570.6 cR 23.2 % 10.3 23 94 UniSTS165123 6.0 cR 597.0 cR 5.8 % 16.6 24 93 UniSTS158888 15.0 cR 603.0 cR 14.0 % 13.9 25 92 UniSTS165120 0.0 cR 618.0 cR 0.0 % 23.5 26 91 UniSTS178507 8.6 cR 618.0 cR 8.3 % 17.1 27 90 UniSTS163270 0.0 cR 626.6 cR 0.0 % 22.3 28 89 UniSTS158883 0.0 cR 626.7 cR 0.0 % 22.8 29 88 UniSTS178510 5.8 cR 626.7 cR 5.6 % 16.1 30 87 UniSTS165121 5.8 cR 632.5 cR 5.6 % 16.1 31 86 UniSTS185457 3.1 cR 638.2 cR 3.0 % 20.8 32 85 UniSTS178506 25.1 cR 641.3 cR 22.2 % 11.8 33 84 UniSTS158881 3.6 cR 666.4 cR 3.5 % 17.8 34 83 UniSTS178504 15.1 cR 670.0 cR 14.0 % 10.2 35 82 UniSTS185456 24.2 cR 685.1 cR 21.5 % 7.9 36 81 UniSTS158879 4.9 cR 709.3 cR 4.8 % 15.4 37 80 UniSTS163269 10.3 cR 714.2 cR 9.8 % 13.8 38 79 UniSTS178502 21.4 cR 724.5 cR 19.3 % 10.4 39 78 UniSTS178493 3.6 cR 745.9 cR 3.5 % 17.1 40 77 UniSTS158875 29.1 cR 749.5 cR 25.3 % 10.9 41 76 UniSTS178489 0.0 cR 778.7 cR 0.0 % 19.4 42 75 UniSTS178488 15.1 cR 778.7 cR 14.0 % 12.0 43 74 UniSTS158871 3.5 cR 793.8 cR 3.5 % 18.0 44 73 UniSTS158872 12.7 cR 797.3 cR 11.9 % 13.5 45 72 UniSTS164135 3.1 cR 810.0 cR 3.1 % 18.0 46 71 UniSTS207240 58.6 cR 813.2 cR 44.3 % 2.7 47 70 UniSTS178484 17.2 cR 871.7 cR 15.8 % 8.8 48 69 UniSTS163266 37.7 cR 889.0 cR 31.4 % 5.1 49 68 UniSTS158867 54.3 cR 926.6 cR 41.9 % 3.5 50 67 UniSTS158866 2.9 cR 980.9 cR 2.8 % 19.7 51 66 UniSTS207212 18.5 cR 983.8 cR 16.9 % 13.0 52 65 UniSTS178476 3.0 cR 1002.3 cR 2.9 % 19.2 53 64 UniSTS158862 111.2 cR 1005.3 cR 67.1 % 2.0 54 63 UniSTS163264 4.5 cR 1116.4 cR 4.4 % 18.8 55 62 UniSTS158857 4.7 cR 1120.9 cR 4.6 % 19.2 56 61 UniSTS165105 35.0 cR 1125.6 cR 29.5 % 10.1 57 60 UniSTS164129 2.6 cR 1160.6 cR 2.6 % 21.7 58 59 UniSTS178466 5.2 cR 1163.3 cR 5.1 % 19.0 59 58 UniSTS158854 29.5 cR 1168.5 cR 25.6 % 10.6 60 57 UniSTS163262 18.7 cR 1198.0 cR 17.0 % 14.1 61 56 UniSTS158849 26.2 cR 1216.7 cR 23.0 % 11.8 62 55 UniSTS178462 18.8 cR 1242.9 cR 17.1 % 12.8 63 54 UniSTS178459 12.9 cR 1261.7 cR 12.1 % 12.9 64 53 UniSTS207204 58.9 cR 1274.6 cR 44.5 % 4.3 65 52 UniSTS158845 19.3 cR 1333.5 cR 17.5 % 12.1 66 51 UniSTS178453 28.1 cR 1352.7 cR 24.5 % 10.8 67 49 UniSTS158844 36.0 cR 1380.8 cR 30.3 % 6.8 68 50 UniSTS178455 94.3 cR 1416.9 cR 61.0 % 1.7 69 48 UniSTS165092 12.5 cR 1511.1 cR 11.8 % 14.1 70 47 UniSTS158832 18.7 cR 1523.6 cR 17.1 % 12.3 71 46 UniSTS178438 50.8 cR 1542.3 cR 39.8 % 5.4 72 45 UniSTS178440 19.3 cR 1593.1 cR 17.6 % 8.8 73 44 UniSTS164122 29.8 cR 1612.4 cR 25.8 % 8.5 74 43 UniSTS158829 29.5 cR 1642.2 cR 25.6 % 10.2 75 42 UniSTS178436 29.9 cR 1671.7 cR 25.9 % 10.3 76 41 UniSTS158825 11.9 cR 1701.7 cR 11.2 % 16.3 77 40 UniSTS165088 33.4 cR 1713.6 cR 28.4 % 9.7 78 39 UniSTS158822 8.8 cR 1747.0 cR 8.4 % 18.2 79 38 UniSTS178427 8.7 cR 1755.8 cR 8.4 % 18.8 80 37 UniSTS178428 5.9 cR 1764.5 cR 5.7 % 17.9 81 36 UniSTS178431 8.9 cR 1770.4 cR 8.5 % 14.9 82 35 UniSTS158824 14.2 cR 1779.4 cR 13.2 % 13.8 83 34 UniSTS178430 45.0 cR 1793.5 cR 36.2 % 8.8 84 33 UniSTS158820 90.1 cR 1838.5 cR 59.4 % 3.7 85 32 UniSTS178422 64.4 cR 1928.6 cR 47.5 % 4.8 86 31 UniSTS178419 46.4 cR 1993.0 cR 37.1 % 6.7 87 30 UniSTS163255 24.4 cR 2039.4 cR 21.6 % 11.7 88 29 UniSTS158816 81.0 cR 2063.8 cR 55.5 % 1.7 89 28 UniSTS207229 59.7 cR 2144.7 cR 45.0 % 4.8 90 27 UniSTS158815 10.2 cR 2204.5 cR 9.7 % 16.4 91 26 UniSTS163252 2.7 cR 2214.7 cR 2.6 % 20.2 92 25 UniSTS158814 9.1 cR 2217.3 cR 8.7 % 16.8 93 24 UniSTS158812 23.1 cR 2226.4 cR 20.6 % 12.5 94 23 UniSTS185438 12.5 cR 2249.5 cR 11.8 % 15.0 95 22 UniSTS178413 28.8 cR 2262.0 cR 25.0 % 11.4 96 21 UniSTS158808 5.7 cR 2290.8 cR 5.6 % 19.3 97 20 UniSTS178410 8.1 cR 2296.5 cR 7.8 % 18.0 98 19 UniSTS158806 8.6 cR 2304.6 cR 8.3 % 18.6 99 18 UniSTS178411 30.6 cR 2313.2 cR 26.4 % 11.2 100 17 UniSTS165083 15.6 cR 2343.8 cR 14.4 % 13.9 101 16 UniSTS158805 0.0 cR 2359.4 cR 0.0 % 22.5 102 15 UniSTS178408 145.4 cR 2359.4 cR 76.6 % 1.3 103 14 UniSTS163250 29.5 cR 2504.8 cR 25.6 % 10.6 104 13 UniSTS178397 27.2 cR 2534.3 cR 23.8 % 11.8 105 12 UniSTS158798 8.2 cR 2561.5 cR 7.9 % 18.8 106 11 UniSTS158795 113.7 cR 2569.7 cR 67.9 % 1.8 107 10 UniSTS178380 4.0 cR 2683.4 cR 3.9 % 22.2 108 9 UniSTS158790 3.8 cR 2687.4 cR 3.7 % 21.9 109 8 UniSTS178382 8.0 cR 2691.2 cR 7.7 % 18.6 110 7 UniSTS158789 --------- 2699.2 cR 110 markers, log10-likelihood = -996.05 log-e-likelihood = -2293.49 retention proba. = 0.27 37 CG>
Thomas Schiex 2018-03-23