Table 1. Comparisons of ancestral inferences using RABBIT, GAIN, and HAPPY.

		RABBIT
Probability	Simulated data set	jointModel	indepModel	depModel	GAIN	HAPPY (diploid)	HAPPY (haploid)
Wrongly assigned	MAGIC-F5	0.143	0.143	0.935	NA	0.779	0.949
	MAGIC-F11	0.096	0.144	0.106	NA	0.446	0.323
	CC-F11-AA	0.027	0.036	0.209	0.037	0.196	0.243
	CC-F22-AA	0.024	0.038	0.046	0.032	0.123	0.090
	CC-F11-XX	0.013	0.017	0.185	0.032	0.160	0.208
	CC-F22-XX	0.011	0.019	0.029	0.027	0.078	0.058
Wrongly called	MAGIC-F5	0.105	0.105	0.934	NA	0.225	0.937
	MAGIC-F11	0.074	0.121	0.085	NA	0.200	0.129
	CC-F11-AA	0.020	0.028	0.205	0.020	0.050	0.214
	CC-F22-AA	0.018	0.030	0.040	0.016	0.051	0.050
	CC-F11-XX	0.008	0.012	0.182	0.014	0.031	0.188
	CC-F22-XX	0.008	0.014	0.026	0.011	0.027	0.032
Pedigree inconsistency	CC-F11-AA	0.00075	0.0040	0	0	0.026	0
	CC-F22-AA	0.00017	0.0039	0	0	0.015	0
	CC-F11-XX	0.00031	0.0014	0	0	0.020	0
	CC-F22-XX	0.00017	0.0017	0	0	0.009	0