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/PAMLdat/jones-dcmut.dat

http://github.com/sbotond/phylosim
Unknown | 50 lines | 38 code | 12 blank | 0 comment | 0 complexity | 6ce233af412c46f1537047c71282f259 MD5 | raw file
 10.531678 
 20.557967 0.451095 
 30.827445 0.154899 5.549530 
 40.574478 1.019843 0.313311 0.105625 
 50.556725 3.021995 0.768834 0.521646 0.091304 
 61.066681 0.318483 0.578115 7.766557 0.053907 3.417706 
 71.740159 1.359652 0.773313 1.272434 0.546389 0.231294 1.115632 
 80.219970 3.210671 4.025778 1.032342 0.724998 5.684080 0.243768 0.201696 
 90.361684 0.239195 0.491003 0.115968 0.150559 0.078270 0.111773 0.053769 0.181788 
100.310007 0.372261 0.137289 0.061486 0.164593 0.709004 0.097485 0.069492 0.540571 2.335139 
110.369437 6.529255 2.529517 0.282466 0.049009 2.966732 1.731684 0.269840 0.525096 0.202562 0.146481 
120.469395 0.431045 0.330720 0.190001 0.409202 0.456901 0.175084 0.130379 0.329660 4.831666 3.856906 0.624581 
130.138293 0.065314 0.073481 0.032522 0.678335 0.045683 0.043829 0.050212 0.453428 0.777090 2.500294 0.024521 0.436181 
141.959599 0.710489 0.121804 0.127164 0.123653 1.608126 0.191994 0.208081 1.141961 0.098580 1.060504 0.216345 0.164215 0.148483 
153.887095 1.001551 5.057964 0.589268 2.155331 0.548807 0.312449 1.874296 0.743458 0.405119 0.592511 0.474478 0.285564 0.943971 2.788406 
164.582565 0.650282 2.351311 0.425159 0.469823 0.523825 0.331584 0.316862 0.477355 2.553806 0.272514 0.965641 2.114728 0.138904 1.176961 4.777647 
170.084329 1.257961 0.027700 0.057466 1.104181 0.172206 0.114381 0.544180 0.128193 0.134510 0.530324 0.089134 0.201334 0.537922 0.069965 0.310927 0.080556 
180.139492 0.235601 0.700693 0.453952 2.114852 0.254745 0.063452 0.052500 5.848400 0.303445 0.241094 0.087904 0.189870 5.484236 0.113850 0.628608 0.201094 0.747889 
192.924161 0.171995 0.164525 0.315261 0.621323 0.179771 0.465271 0.470140 0.121827 9.533943 1.761439 0.124066 3.038533 0.593478 0.211561 0.408532 1.143980 0.239697 0.165473 
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220.076862 0.051057 0.042546 0.051269 0.020279 0.041061 0.061820 0.074714 0.022983 0.052569 0.091111 0.059498 0.023414 0.040530 0.050532 0.068225 0.058518 0.014336 0.032303 0.066374
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25 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
26Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
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29JTT rate matrix prepared using the DCMut method*
30------------------------------------------------
31
32The first part above indicates the symmetric 'exchangeability' parameters s_ij, 
33where s_ij = s_ji.
34The second part gives the amino acid equilibrium frequencies pi_i. 
35The net replacement rate from i to j is q_ij = pi_j*s_ij.
36        
37This model is usually scaled so that the mean rate of change at
38equilibrium, Sum_i Sum_j!=i pi_i*q_ij, equals 1.  You should check this
39scaling before using the matrix above.  The PAML package will perform
40this scaling.
41
42//
43
44*Prepared by Carolin Kosiol and Nick Goldman, December 2003.
45
46See the following paper for more details:
47Kosiol, C., and Goldman, N. 2005. Different versions of the Dayhoff rate matrix. 
48Molecular Biology and Evolution 22:193-199.
49
50See also http://www.ebi.ac.uk/goldman/dayhoff