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