Positive selection in the hemagglutinin-neuraminidase gene of Newcastle disease virus and its effect on vaccine efficacy

Table 2 Parameter estimates and likelihood values corresponding to the results from different models

Model	lnL	dN/dS	Estimated parameters	Df^a	2△l^b	Positively selected codons^c
M0 (one-ratio)	-13384.287	0. 225	ω = 0. 225	4		None
M3 (discrete)	-13246. 011	0. 228	p₀= 0.656, p₁= 0.310, p₂= 0.034 ω₀= 0.069, ω₁= 0.446, ω₂ = 1.313^d		276.552 (p < 0.01)	266, 347, 540
M7 (beta)	-13253. 972	0. 227	p = 0.486, q = 1.635	2		Not allowed
M8 (beta& ω)	-13247. 102	0. 228	p₀= 0.968, p₁= 0.032 p = 0.662, q = 2.730, ω = 1.312		13.740 (p < 0.01)	266, 347, 540

^a Df: degree of freedom.
^b 2△l: Log likelihood difference between nested models using the χ2-test.
^c Codons estimated to be under positive selection at the 90% level. Numbers in bold denote codons with posterior probabilities over 95%.
^d Underlined parameters are evidence of positive selection.

ISSN: 1743-422X