Experimental Results on Some Test Files (Superlink v1.2)

(updated March 30th 2003)


Experiment 1: (The pedigree topology is taken from pedigree B in Kruglyak et al., 1996, the marker data is simulated. We used both increasing number of loci and increasing number of untyped individuals.)

This is a complex inbred pedigree that occurred in the study of Werner syndrome (Thompson and Wisjman 1994). The pedigree has 15 people (with inbreeding loops). All the markers have 5-10 alleles.
 

Files (Superlink)
pedfile (Genehunter)
Graphical
Representation
(bmp)
 #Loci
%Typed
Individuals
Ln-Likelihood/
LodScore
Run Time
Superlink 1.1
Run Time Superlink 1.2
Run Time
Vitesse
Run Time
Genehunter
dataGB_90_0/pedGB_90_0
pedGB_90_0
pedGB_90_0
 2
90
 -30.765648 /-0.009104
 1.359s
0.006s
 ***
 26.859s (#)
dataGB_90_1/pedGB_90_1
pedfileGB_90_1
pedGB_90_1
 4
90
 -61.979443/-0.010976
 1.451s
0.004s
 ***
 28.088s (#)
dataGB_90_2/pedGB_90_2
pedGB_90_2
pedGB_90_2
 6
90
 -87.162344/-0.010976
 1.194s
0.006s
 ***
 29.184s (#)
dataGB_90_3/pedGB_90_3
pedGB_90_3
pedGB_90_3
8
90
 -126.225294/-0.010976
 1.463s
0.008s
***
 30.453s (#)
dataGB_67_0/pedGB_67_0
pedGB_67_0
pedGB_67_0
2
67
-19.899434/0.158507
24.982s/
1m10.478s
0.016s/0.0014s
***
26.722s (#)
dataGB_67_1/pedGB_67_1
pedfileGB_67_1
pedGB_67_1
4
67
 -44.296082/0.196442
*****
1m35.814s/
1m32.870s
***
28.895s (#)
dataGB_67_2/pedGB_67_2
pedGB_67_2
pedGB_67_2
6
67
-67.511774/0.225099
*****
8m4.442s/
7m58.221s/
6m4.631s
***
30.198s (#)
dataGB_67_3/pedGB_67_3
pedGB_67_3
pedGB_67_3
8
67
-102.286050/0.034458
8m05.600s/
3m11.510s
***
31.693s (#)
dataGB_27_0/pedGB_27_0
pedGB_27_0
pedGB_27_0
2
27
-6.595469/0.000000
56.67s/56.812s
0.004s
***
26.912s (#)
dataGB_27_1/pedGB_27_1
pedGB_27_1
pedGB_27_1
4
27
-20.055220/0.000000
*****
30.07s/39.179s
***
29.280s (#)
dataGB_27_2/pedGB_27_2
pedGB_27_2
pedGB_27_2
6
27
-41.643023/0.000000
*****
1hr44m17.370s
***
30.949s (#)
dataGB_27_3/pedGB_27_3
pedGB_27_3
pedGB_27_3
8
27
-51.035190/0.000000
*****
1hr19m54.666s/
23m19.440s
***
32.414s (#)

 

Experiment 2:(The pedigree topology is taken from pedigree C in Kruglyak et al., 1996, the marker data is simulated. We used both increasing number of loci and increasing number of untyped individuals.)

This pedigree has 29 people (with no inbreeding loops). All the markers have 5-10 alleles.
 

Files (Superlink)
pedfile (Genehunter)
Graphical
Representation
 #Loci
%Typed
Individuals
Ln-Likelihood/
LodScore
Run Time
Superlink 1.1
Run Time Superlink 1.2
Run Time
Vitesse
Run Time
Genehunter
dataGC_86_0/pedGC_86_0
ped_GC_86_0
pedGC_86_0
2
86
-52.009978/-0.001761
0.024s
0.008s
0.041s
 3.666s (#) 
dataGC_86_1/pedGC_86_1
ped_GC_86_1
pedGC_86_1
4
86
-151.800991/0.002835
 0.024s
 0.014s
 0.041s
 11.086s (#)
dataGC_86_2/pedGC_86_2
ped_GC_86_2
pedGC_86_2
6
86
-254.033001/0.003109
 0.031s
 0.016s
 0.067s
 16.922s (#)
dataGC_86_3/pedGC_86_3
ped_GC_86_3
pedGC_86_3
8
86
-329.052586/0.003116
 0.053s
 0.053s
 5.637s
 22.894s (#)
dataGC_69_0/pedGC_69_0
ped_GC_69_0
pedGC_69_0
2
69
-56.408059/-0.014804
 0.023s
0.006s 
 0.050s
 1.510s (#)
dataGC_69_1/pedGC_69_1
ped_GC_69_1
pedGC_69_1
4
69
-119.151764/0.034879
 0.239s
 0.232s
 0.063s
 9.246s (#)
dataGC_69_21/pedGC_69_2
ped_GC_69_2
pedGC_69_2
6
69
-174.062217/0.033061
 0.711s
 0.347s
 0.347s
 15.168s (#)
dataGC_69_3/pedGC_69_3
ped_GC_69_3
pedGC_69_3
8
69
-235.769002/0.034138 
 1.357s
0.008s
 0.427s
 24.928s (#)
dataGC_31_0/pedGC_31_0
ped_GC_31_0
pedGC_31_0
2
31
-15.180639/0.000201
 0.194s/ 0.145s
 0.006s
 0.053s
 3.088s (#)
dataGC_31_1/pedGC_31_1
ped_GC_31_1
pedGC_31_1
4
31
-58.735612/-0.000416
 2m31.553s  1m6.028s/21.990s/
5.95s/5.98s
 26.621s
 10.254s (#)
dataGC_31_2/pedGC_31_2
ped_GC_31_2
pedGC_31_2
6
31
-100.226173/-0.000335
*****
 31m43.240s/
28m42.928s
 *****
 17.571s (#)
dataGC_31_3/pedGC_31_3
ped_GC_31_3
pedGC_31_3
8
31
 
 
 *****
 
 25.395s (#)

 Clarifications to the tables:

References:
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