Table 2.

Model A parameter estimates for significant branch-site LRTs.

Cluster	Lineage	Site Class	Proportion	Backgound ω	Foreground ω	Positively Selected Sites* (P ≥ 0.95)
FoxA	FoxA3	0	0.63948	0.02356	0.02356	FOXA3_hsap 27P, 36G, 112P, 113L
		1	0.330014	1	1
		2a	0.04109	0.02356	999
		2b	0.01929	1	999
	Protostomia	0	0.62704	0.02362	0.02362	FOXA1_hsap 68Y, 159A, 199W, 234S, 237K, 242S
		1	0.29309	1	1
		2a	0.05443	0.02362	999
		2b	0.02554	1	999
FoxD	FoxD1/2/4	0	0.53693	0.02506	0.02506	FOXD2_hsap R390
		1	0.41932	1	1
		2a	0.0456	0.02506	71.85587
		2b	0.01918	1	71.85587
	FoxD2	0	0.51695	0.02526	0.02526	FOXD2_hsap E242, T386, L389, R390, Q391, G392, L393, K394, T395
		1	0.36815	1	1
		2a	0.06711	0.02526	999
		2b	0.04779	1	999
FoxO	FoxO3	0	0.80461	0.04277	0.04277	FOXO3_hsap S280
		1	0.14422	1	1
		2a	0.04339	0.04277	10.7599
		2b	0.00778	1	10.7599

* The sequence to which amino acid residues reported correspond is given for each lineage.