Table 4.

Comparison of the estimation of the linkage and gene order between three dominant markers in a full-sib family of n = 100 from the traditional and our model

MLE	Traditional model			Our model
Data stimulated from [aaa] [ooo] × [aaa] [ooo]
Correct gene order	Correct	Incorrect	Incorrect
Estimated best gene order (%a)	100	0	0
	0.2047 ± 0.0422			0.2048 ± 0.0422
	0.1980 ± 0.0436			0.1985 ± 0.0434
	0.3245 ± 0.0619			0.3235 ± 0.0618
				0.9860 ± 0.0105
				0.0060 ± 0.0071
				0.0080 ± 0.0079
Data simulated from [aao] [ooa] × [aao] [ooa]
Correct gene order	Correct	Incorrect	Incorrect
Estimated best gene order (%a)	80	11	9
	0.1991 ± 0.0456	0.8165 ± 0.1003	0.9284 ± 0.0724	0.2104 ± 0.0447
	0.1697 ± 0.0907	0.8220 ± 0.0338	0.1636 ± 0.0608	0.2073 ± 0.0754
	0.3218 ± 0.0755	0.2703 ± 0.0586	0.7821 ± 0.0459	0.2944 ± 0.0929
				0.9952 ± 0.0058
				0.0045 ± 0.0058
				0.0003 ± 0.0015

^aThe percents of a total of 200 simulations that have a largest likelihood for a given gene order estimated from the traditional approach. In this example used to examine the advantage of implementing gene orders, known linkage phases are assumed.