Table 3.

Site tests of adaptive evolution, fixed class model.

Model	N parameters	All sites		Cytosolic sites		Transmembrane sites		External sites
		ln L	ω Values	lnL	ω Values	lnL	ω Values	lnL	ω Values
A
(A) ‘M0’, one ω class	45	−18039.469	0.19	−9412.785	0.28	−8413.696	0.12	−2462.885	0.20
(B) ‘M1a’, two ω classes (<1,1)	46	−17475.971	0.07, 1.00	−9178.578	0.10, 1.00	−8172.866	0.05, 1.00	−2367.630	0.07, 1.00
(C) ‘M2a’, three ω classes (<1, 1,>1)	48	−17469.195	0.07, 1.00, 2.86	−9178.578	0.10, 1.00, 1.00	−8166.515	0.05, 1.00, 3.12	−2364.868	0.07, 1.00, 2.88

Likelihood ratio tests	All sites			Cytosolic sites			Transmembrane sites			External sites
	2ΔlnL	P value	Selected sites	2ΔlnL	P value	Selected sites	2ΔlnL	P value	Selected sites	2ΔlnL	P value	Selected sites
B
Two ω classes vs. One ω class (A vs. B (df = 1))	1127	0	n/a	468.4	0	n/a	481.7	0	n/a	190.5	0	n/a
Two ω classes vs. Three ω classes (B vs. C (df = 2))	13.6	0.001	367-1a, 658	0	1	n/a	12.7	0.002	658	5.5	0.063	n/a

A: parameters and likelihoods estimated for the different models.

B: likelihood ratio tests described in Sections 2 and 3. Bold indicates P < 0.05.

^aThe position under selection is a gap in the human alignment corresponding to the codon before the 367th codon in human.