Computing Ka and Ks with a consideration of unequal transitional substitutions

Table 4 Proportions of synonymous sites (S%) and estimates of Ka, Ks and ω

Method	κ_R – κ_Y > 1				κ_R – κ_Y < -1				\|κ_R – κ_Y\|≤ 1
	S%	Ka	Ks	ω	S%	Ka	Ks	ω	S%	Ka	Ks	ω
human-mouse orthologs
LPB	-	0.069	0.463	0.148	-	0.071	0.449	0.159	-	0.105	0.500	0.209
GY	27.2%	0.065	0.518	0.125	27.1%	0.068	0.503	0.135	26.9%	0.101	0.561	0.180
YN	27.4%	0.064	0.527	0.121	27.2%	0.067	0.505	0.133	26.6%	0.099	0.588	0.169
MYN	26.1%	0.063	0.597	0.105	28.5%	0.068	0.474	0.144	26.5%	0.099	0.591	0.168
human-dog orthologs
LPB	-	0.055	0.309	0.176	-	0.057	0.296	0.192	-	0.081	0.348	0.233
GY	27.5%	0.052	0.332	0.157	27.5%	0.055	0.318	0.172	26.5%	0.078	0.381	0.205
YN	27.8%	0.052	0.329	0.158	27.8%	0.055	0.310	0.176	26.4%	0.077	0.387	0.200
MYN	26.5%	0.051	0.357	0.143	29.1%	0.056	0.294	0.189	26.3%	0.077	0.389	0.199
mouse-rat orthologs
LPB	-	0.030	0.176	0.173	-	0.030	0.170	0.179	-	0.048	0.196	0.245
GY	28.0%	0.030	0.189	0.157	27.7%	0.029	0.183	0.160	26.9%	0.047	0.214	0.220
YN	28.2%	0.029	0.186	0.157	27.9%	0.029	0.180	0.162	26.6%	0.046	0.216	0.215
MYN	26.6%	0.029	0.201	0.142	29.1%	0.030	0.171	0.173	26.5%	0.046	0.216	0.214

Note: The values were calculated from concatenated sequences according to the three scenarios of κ_R and κ_Y. The methods compared in addition to YN and MYN were LPB, an approximate method developed by Li (1993) and by Pamilo and Bianchi (1993) independently, and GY, a maximum likelihood method proposed by Goldman and Yang (1994). When GY was used, codon frequencies were calculated from nucleotide frequencies of three codon positions.

ISSN: 2730-7182