This file has estimates of dN and dS in pairwise comparisons of sequences in the abglobin.nuc data set. The methods used include that of Nei and Gojobori (1986), implemented in codeml and yn00, the method of Yang and Nielsen (2000), implemented in yn00, as well as the ML method of Goldman and Yang (1994), implemented in codeml. Ziheng Yang ns = 5 ls = 285 Nei & Gojobori 1986. dN/dS (dN, dS) human goat-cow 0.251(0.0863 0.3443) rabbit 0.263(0.0867 0.3301) 0.294(0.1054 0.3581) rat 0.204(0.1261 0.6164) 0.246(0.1493 0.6065) 0.218(0.1348 0.6187) marsupial 0.190(0.1931 1.0148) 0.189(0.1910 1.0099) 0.218(0.2111 0.9668) 0.272(0.2404 0.8852) Pairwise estimation by the method of Yang & Nielsen (2000) (equal weighting of pathways) seq. seq. S N t kappa omega dN dS 2 1 183.7 671.3 0.5169 1.5804 0.1625 0.0818 0.5031 3 1 177.5 677.5 0.5033 1.5804 0.1642 0.0815 0.4967 3 2 180.1 674.9 0.5627 1.5804 0.1929 0.0997 0.5169 4 1 191.3 663.7 0.9075 1.5804 0.1308 0.1216 0.9301 4 2 192.4 662.6 0.9642 1.5804 0.1557 0.1447 0.9297 4 3 187.0 668.0 0.9790 1.5804 0.1262 0.1298 1.0286 5 1 189.3 665.7 2.1638 1.5804 0.0711 0.1853 2.6055 5 2 190.4 664.6 1.2984 1.5804 0.1416 0.1842 1.3008 5 3 185.2 669.8 1.3214 1.5804 0.1554 0.2023 1.3020 5 4 194.5 660.5 1.5554 1.5804 0.1591 0.2354 1.4797 Pairwise estimation by the method of Yang & Nielsen (2000) (weighting) seq. seq. S N t kappa omega dN dS 2 1 183.7 671.3 0.5191 1.5804 0.1573 0.0804 0.5114 3 1 177.5 677.5 0.5034 1.5804 0.1626 0.0811 0.4987 3 2 180.1 674.9 0.5623 1.5804 0.1930 0.0997 0.5165 4 1 191.3 663.7 0.9180 1.5804 0.1253 0.1194 0.9533 4 2 192.4 662.6 1.0073 1.5804 0.1360 0.1382 1.0159 4 3 187.0 668.0 1.0074 1.5804 0.1149 0.1251 1.0886 5 1 189.3 665.7 1.4489 1.5804 0.1114 0.1746 1.5671 5 2 190.4 664.6 1.3918 1.5804 0.1180 0.1741 1.4758 5 3 185.2 669.8 1.4303 1.5804 0.1261 0.1906 1.5118 5 4 194.5 660.5 1.7449 1.5804 0.1252 0.2246 1.7938 pairwise comparison by ML (Goldman & Yang 1994) seq seq S N dN dS dN/dS Paras. 2 1 186.0 669.0 0.0839 0.4309 0.1948 0.4783 2.2914 0.1948 -1508.6 3 1 179.9 675.1 0.0842 0.4247 0.1982 0.4676 2.1904 0.1982 -1512.5 3 2 183.5 671.5 0.1036 0.4570 0.2267 0.5384 2.2643 0.2267 -1557.3 4 1 190.2 664.8 0.1223 0.8097 0.1511 0.8258 1.7892 0.1511 -1649.7 4 2 200.2 654.8 0.1458 0.7773 0.1876 0.8809 2.4058 0.1876 -1677.1 4 3 193.2 661.8 0.1306 0.8105 0.1611 0.8528 2.2165 0.1611 -1666.4 5 1 176.2 678.8 0.1729 3.0396 0.0569 2.2908 0.9866 0.0569 -1769.0 5 2 180.8 674.2 0.1762 2.1879 0.0805 1.8049 1.1964 0.0805 -1774.7 5 3 173.1 681.9 0.1882 2.7162 0.0693 2.0998 1.0659 0.0693 -1794.5 5 4 180.6 674.4 0.2214 1.7973 0.1232 1.6631 1.0212 0.1232 -1842.6