Table 3. ML estimates and AIC values of the present models for the 1-PAM amino acid substitution matrices of JTT, WAG, and LG, and the 1-PAM codon substitution matrix of KHG.

		JTT			WAG			LG		KHG
										(codon)
id	parameter	ML–87a	ML–91a	ML–94	ML–87a	ML–91a	ML–94	ML–91a	ML–94	ML–200
no.
0		N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A
1		N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A
2		()	0.637	0.662	()	1.28	1.29	1.08	1.19	0.939
3		0.0919	1.57	1.59	0.746	1.70	1.69	1.85	1.81	0.843
4		1.77	1.14	1.15	1.98	1.32	1.31	1.23	1.21	0.945
5		0.0293	0.729	0.730	0.0477	0.791	0.784	0.676	0.682	1.52
6		3.21	0.940	0.950	3.64	1.04	1.01	1.07	1.07	0.554
7		0.719	1.19	1.18	0.110	1.23	1.23	1.28	1.25	0.573
8		0.408	0.459	0.446	0.372	0.367	0.392	0.388	0.403	0.497
9		0.113	0.501	0.522	0.234	0.587	0.513	0.450	0.439	0.513
10		0.698	0.429	0.436	0.425	0.479	0.471	0.427	0.383	0.470
11		0.0682	(0.5)	0.483	0.0669	(0.5)	0.221	(0.5)	0.447	NA
12		0.461	(0.5)	0.491	0.330	(0.5)	0.429	(0.5)	0.555	NA
13		0.386	(0.5)	0.558	0.310	(0.5)	0.306	(0.5)	0.249	NA
14		27.3	0.738	0.740	43.3	0.905	0.840	0.415	0.395
		0.334	0.0243	0.0246	0.317	0.0223	0.0207	0.0246	0.0240	0.0240
#parameters		107	111	114	107	111	114	111	114	261
b			638			1903		2771	2335	269946
c		2072.0	297.5	300.6	1370.8	284.3	275.1	782.5	700.4	unknown
Ratio of substitution rates
per codon
the total base/codon		1.28	1.35	1.35	1.38	1.53	1.52	1.38	1.39	1.29
										(1.29)d
transition/transversion		0.464	1.08	1.08	0.482	0.932	0.806	1.18	1.20	0.764
										(0.765)d
nonsynonymous/synonymouse		1.13	1.37	1.34	1.57	2.07	2.40	1.05	1.20	0.726
										(0.723)d
Ratio of substitution rates
per codon for
total base/codon		1.0	1.22	1.22	1.0	1.38	1.40	1.31	1.33	1.29
transition/transversion		0.101	1.21	1.22	0.647	1.11	0.932	1.31	1.35	0.764
nonsynonymous/synonymouse		0.0644	1.04	1.02	0.138	1.50	1.79	0.853	0.889	0.726
Ratio of substitution rates per
codon for and
total base/codon		1.0	1.45	1.46	1.0	1.72	1.74	1.67	1.71	1.51
transition/transversion		0.0605	0.829	0.831	0.499	0.933	0.849	0.992	0.981	0.427
nonsynonymous/synonymouse		11.3	5.58	5.74	11.1	8.68	11.1	7.45	8.46	6.81

^aIf the value of a parameter is parenthesized, the parameter is not variable but fixed to the value specified.

^b for JTT, for WAG, for LG, and for KHG; see text for details.

^c #parameters with for JTT, for WAG, for LG, and the value of is unknown for KHG; see text for details.

^dThe value in the parenthesis corresponds to the one for the KHG codon substitution probability matrix.

^eNote that these ratios are not the ratios of the rates per site but per codon; see text for details.