TABLE B1.

Performance for models with uniform recombination rates with phased data

γa	ρa	g(γ)b	g(ρ)b	B(γ)c	B(ρ)c	E()d	E()d	V(γ)e	V(ρ)e
Hudson's composite likelihood method
5	5	0.246	0.696	0.555	0.611	8.917	5.097	2.842	0.994
10	10	0.324	0.828	0.609	0.580	12.590	11.140	1.769	0.829
20	20	0.368	0.792	0.671	0.590	19.250	21.650	1.274	0.770
40	40	0.468	0.874	0.638	0.512	34.880	43.490	0.936	0.591
80	80	0.460	0.840	0.691	0.490	59.820	92.520	0.766	0.624
100	100	0.518	0.820	0.665	0.462	77.190	115.04	0.727	0.604
Summary statistics method: acceptance rate = 15%
5	5	0.265	0.647	0.547	0.408	12.1873	9.7706	4.619	4.024
10	10	0.398	0.766	0.589	0.520	14.7102	13.4611	2.075	1.590
20	20	0.483	0.816	0.594	0.572	23.1785	21.957	1.282	0.771
40	40	0.588	0.868	0.476	0.462	48.44	44.90	1.046	0.639
80	80	0.576	0.850	0.488	0.479	91.54	90.08	0.843	0.581
100	100	0.648	0.852	0.480	0.472	109.68	112.82	0.742	0.563
Summary statistics method: acceptance rate = 30%
5	5	0.242	0.746	0.574	0.394	7.768	5.735	2.402	0.914
10	10	0.358	0.842	0.533	0.588	14.230	10.543	1.752	0.694
20	20	0.522	0.842	0.580	0.601	22.717	20.810	1.215	0.662
40	40	0.638	0.888	0.543	0.498	43.060	43.540	0.937	0.567
80	80	0.604	0.860	0.514	0.534	89.060	86.640	0.839	0.562
100	100	0.652	0.846	0.484	0.491	109.58	109.32	0.743	0.554
Summary statistics method: acceptance rate = 60%
5	5	0.233	0.783	0.565	0.463	6.913	4.856	2.020	0.754
10	10	0.407	0.832	0.568	0.656	12.446	9.655	1.514	0.631
20	20	0.555	0.823	0.571	0.673	23.043	18.874	1.197	0.558
40	40	0.654	0.908	0.567	0.593	39.66	39.10	0.858	0.496
80	80	0.634	0.872	0562	0.623	80.14	79.12	0.739	0.520
100	100	0.68	0.822	0.570	0.556	98.66	101.74	0.690	0.539