Table 2.

Estimation of d_N and d_S between the human and orangutan α2-globin genes (142 codons)^a

Method and/or model	k	S	N	dN	dS	dN/dS (v)	lc	Refs
Approximate methods
Nei and Gojobori	1.0	109.4	316.6	0.0095	0.0569	0.168	–	9
Li	–	NA	NA	0.0104	0.0517	0.201	–	11
Ina	2.1	119.3	299.9	0.0101	0.0523	0.193	–	14
Yang and Nielsen	6.1	61.7	367.3	0.0083	0.1065	0.078	–	15
ML methodsb
(1) Fequal, k=1	1.0	108.5	317.5	0.0093	0.0557	0.167	−633.67	16
(2) Fequal, k estimated	3.0	124.6	301.4	0.0099	0.0480	0.206	−632.47	16
(3) F1×4, k=1 fixed	1.0	129.1	296.9	0.0092	0.0671	0.137	−612.40	16
(4) F1×4, k estimated	3.9	137.1	288.9	0.0093	0.0624	0.149	−610.48	16
(5) F3×4, k=1 fixed	1.0	63.2	362.8	0.0084	0.0973	0.087	−560.76	16
(6) F3×4, k estimated	5.4	60.6	365.4	0.0084	0.1061	0.079	−557.85	16
(7) F61, k=1 fixed	1.0	58.3	367.7	0.0082	0.1145	0.072	−501.39	16
(8) F61, k estimated	5.3	55.3	370.7	0.0082	0.1237	0.066	−498.61	16

^aGenBank accession numbers are V00516 (human) and M12158 (orangutan).

^bFequal, equal codon frequencies (=1/61) are assumed; F1×4, four nucleotide frequencies are used to calculate codon frequencies (3 free parameters); F3×4, nucleotide frequencies at three codon positions are used to calculate codon frequencies (9 free parameters); F61, all codon frequencies are used as free parameters (60 free parameters).

^cl is the log-likelihood value.