1 This file has estimates of dN and dS in pairwise comparisons of
\r
2 sequences in the abglobin.nuc data set. The methods used include that
\r
3 of Nei and Gojobori (1986), implemented in codeml and yn00, the method
\r
4 of Yang and Nielsen (2000), implemented in yn00, as well as the ML
\r
5 method of Goldman and Yang (1994), implemented in codeml.
\r
12 Nei & Gojobori 1986. dN/dS (dN, dS)
\r
14 goat-cow 0.251(0.0863 0.3443)
\r
15 rabbit 0.263(0.0867 0.3301) 0.294(0.1054 0.3581)
\r
16 rat 0.204(0.1261 0.6164) 0.246(0.1493 0.6065) 0.218(0.1348 0.6187)
\r
17 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)
\r
19 Pairwise estimation by the method of Yang & Nielsen (2000)
\r
20 (equal weighting of pathways)
\r
22 seq. seq. S N t kappa omega dN dS
\r
24 2 1 183.7 671.3 0.5169 1.5804 0.1625 0.0818 0.5031
\r
25 3 1 177.5 677.5 0.5033 1.5804 0.1642 0.0815 0.4967
\r
26 3 2 180.1 674.9 0.5627 1.5804 0.1929 0.0997 0.5169
\r
27 4 1 191.3 663.7 0.9075 1.5804 0.1308 0.1216 0.9301
\r
28 4 2 192.4 662.6 0.9642 1.5804 0.1557 0.1447 0.9297
\r
29 4 3 187.0 668.0 0.9790 1.5804 0.1262 0.1298 1.0286
\r
30 5 1 189.3 665.7 2.1638 1.5804 0.0711 0.1853 2.6055
\r
31 5 2 190.4 664.6 1.2984 1.5804 0.1416 0.1842 1.3008
\r
32 5 3 185.2 669.8 1.3214 1.5804 0.1554 0.2023 1.3020
\r
33 5 4 194.5 660.5 1.5554 1.5804 0.1591 0.2354 1.4797
\r
36 Pairwise estimation by the method of Yang & Nielsen (2000)
\r
39 seq. seq. S N t kappa omega dN dS
\r
41 2 1 183.7 671.3 0.5191 1.5804 0.1573 0.0804 0.5114
\r
42 3 1 177.5 677.5 0.5034 1.5804 0.1626 0.0811 0.4987
\r
43 3 2 180.1 674.9 0.5623 1.5804 0.1930 0.0997 0.5165
\r
44 4 1 191.3 663.7 0.9180 1.5804 0.1253 0.1194 0.9533
\r
45 4 2 192.4 662.6 1.0073 1.5804 0.1360 0.1382 1.0159
\r
46 4 3 187.0 668.0 1.0074 1.5804 0.1149 0.1251 1.0886
\r
47 5 1 189.3 665.7 1.4489 1.5804 0.1114 0.1746 1.5671
\r
48 5 2 190.4 664.6 1.3918 1.5804 0.1180 0.1741 1.4758
\r
49 5 3 185.2 669.8 1.4303 1.5804 0.1261 0.1906 1.5118
\r
50 5 4 194.5 660.5 1.7449 1.5804 0.1252 0.2246 1.7938
\r
52 pairwise comparison by ML (Goldman & Yang 1994)
\r
54 seq seq S N dN dS dN/dS Paras.
\r
56 2 1 186.0 669.0 0.0839 0.4309 0.1948 0.4783 2.2914 0.1948 -1508.6
\r
57 3 1 179.9 675.1 0.0842 0.4247 0.1982 0.4676 2.1904 0.1982 -1512.5
\r
58 3 2 183.5 671.5 0.1036 0.4570 0.2267 0.5384 2.2643 0.2267 -1557.3
\r
59 4 1 190.2 664.8 0.1223 0.8097 0.1511 0.8258 1.7892 0.1511 -1649.7
\r
60 4 2 200.2 654.8 0.1458 0.7773 0.1876 0.8809 2.4058 0.1876 -1677.1
\r
61 4 3 193.2 661.8 0.1306 0.8105 0.1611 0.8528 2.2165 0.1611 -1666.4
\r
62 5 1 176.2 678.8 0.1729 3.0396 0.0569 2.2908 0.9866 0.0569 -1769.0
\r
63 5 2 180.8 674.2 0.1762 2.1879 0.0805 1.8049 1.1964 0.0805 -1774.7
\r
64 5 3 173.1 681.9 0.1882 2.7162 0.0693 2.0998 1.0659 0.0693 -1794.5
\r
65 5 4 180.6 674.4 0.2214 1.7973 0.1232 1.6631 1.0212 0.1232 -1842.6
\r