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Precisely describes the best map in the current Pareto frontier.
The paretobestprintd command is invoked as:
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 2009-10-27