/PAMLdat/jones-dcmut.dat

http://github.com/sbotond/phylosim · Unknown · 50 lines · 38 code · 12 blank · 0 comment · 0 complexity · 6ce233af412c46f1537047c71282f259 MD5 · raw file

  1. 0.531678
  2. 0.557967 0.451095
  3. 0.827445 0.154899 5.549530
  4. 0.574478 1.019843 0.313311 0.105625
  5. 0.556725 3.021995 0.768834 0.521646 0.091304
  6. 1.066681 0.318483 0.578115 7.766557 0.053907 3.417706
  7. 1.740159 1.359652 0.773313 1.272434 0.546389 0.231294 1.115632
  8. 0.219970 3.210671 4.025778 1.032342 0.724998 5.684080 0.243768 0.201696
  9. 0.361684 0.239195 0.491003 0.115968 0.150559 0.078270 0.111773 0.053769 0.181788
  10. 0.310007 0.372261 0.137289 0.061486 0.164593 0.709004 0.097485 0.069492 0.540571 2.335139
  11. 0.369437 6.529255 2.529517 0.282466 0.049009 2.966732 1.731684 0.269840 0.525096 0.202562 0.146481
  12. 0.469395 0.431045 0.330720 0.190001 0.409202 0.456901 0.175084 0.130379 0.329660 4.831666 3.856906 0.624581
  13. 0.138293 0.065314 0.073481 0.032522 0.678335 0.045683 0.043829 0.050212 0.453428 0.777090 2.500294 0.024521 0.436181
  14. 1.959599 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
  15. 3.887095 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
  16. 4.582565 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
  17. 0.084329 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
  18. 0.139492 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
  19. 2.924161 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
  20. 0.076862 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
  21. A R N D C Q E G H I L K M F P S T W Y V
  22. Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
  23. JTT rate matrix prepared using the DCMut method*
  24. ------------------------------------------------
  25. The first part above indicates the symmetric 'exchangeability' parameters s_ij,
  26. where s_ij = s_ji.
  27. The second part gives the amino acid equilibrium frequencies pi_i.
  28. The net replacement rate from i to j is q_ij = pi_j*s_ij.
  29. This model is usually scaled so that the mean rate of change at
  30. equilibrium, Sum_i Sum_j!=i pi_i*q_ij, equals 1. You should check this
  31. scaling before using the matrix above. The PAML package will perform
  32. this scaling.
  33. //
  34. *Prepared by Carolin Kosiol and Nick Goldman, December 2003.
  35. See the following paper for more details:
  36. Kosiol, C., and Goldman, N. 2005. Different versions of the Dayhoff rate matrix.
  37. Molecular Biology and Evolution 22:193-199.
  38. See also http://www.ebi.ac.uk/goldman/dayhoff