Table 1.

The percentage of superfamilies that are consistent with the perfect phylogeny (PP), Static Dollo parsimony (SDP) and conservative Dollo parsimony (CDP) criteria. Databases marked ”(c)” include only super-families meeting complex criteria. ”num domains” indicates that only superfamilies with the specified number of domains in their domain overlap graph were included. ”num super” indicates the number of superfamilies meeting these criteria. % Unif, % PA, and %FD refer to the expected percentage of families admitting a Conservative Dollo parsimony under the uniform, preferential attachment, and fixed degree (endpoint swapping) null models. NE indicates a quantity not estimated.

Database	num domains	num super	%PP	%SDP	%CDP	%Unif	%PA	%FD
Mouse	*	983	95	99	99.7	NE	NE	NE
Mouse (c)	4-5	88	99	100	100	80	98	100
Mouse (c)	6-8	37	84	100	100	31	66	73
Mouse (c)	9-10	11	66	100	100	17	25	54
Mouse (c)	11-20	23	31	96	96	1.7	1.0	21
Mouse (c)	21-30	9	0	66	100	0	0	0
Mouse (c)	31-*	8	0	50	75	0	0	0
Nr90	*	2896	80	98	99.9	NE	NE	NE
Nr90 (c)	4-5	143	57	99	99.5	80	98	99
Nr90 (c)	6-8	130	37	99	100	31	66	89
Nr90 (c)	9-10	40	28	100	100	17	25	74
Nr90 (c)	11-20	104	13	87	99	1.7	1.0	26
Nr90 (c)	21-30	34	6	53	88	0	0	2.9
Nr90 (c)	30-*	28	0	15	50	0	0	0
Human Kin	*	101	11	100	100	NE	NE	NE