/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. 

  2. 0.557967 0.451095 

    3. 

  3. 0.827445 0.154899 5.549530 

    4. 

  4. 0.574478 1.019843 0.313311 0.105625 

    5. 

  5. 0.556725 3.021995 0.768834 0.521646 0.091304 

    6. 

  6. 1.066681 0.318483 0.578115 7.766557 0.053907 3.417706 

    7. 

  7. 1.740159 1.359652 0.773313 1.272434 0.546389 0.231294 1.115632 

    8. 

  8. 0.219970 3.210671 4.025778 1.032342 0.724998 5.684080 0.243768 0.201696 

    9. 

  9. 0.361684 0.239195 0.491003 0.115968 0.150559 0.078270 0.111773 0.053769 0.181788 

    10. 

  10. 0.310007 0.372261 0.137289 0.061486 0.164593 0.709004 0.097485 0.069492 0.540571 2.335139 

    11. 

  11. 0.369437 6.529255 2.529517 0.282466 0.049009 2.966732 1.731684 0.269840 0.525096 0.202562 0.146481 

    12. 

  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. 

  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. 

  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. 

  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. 

  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. 

  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. 

  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. 

  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. 

  20. 

    21. 

  21. 

    22. 

  22. 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

    23. 

  23. 

    24. 

  24. 

    25. 

  25.  A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V

    26. 

  26. Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val

    27. 

  27. 

    28. 

  28. 

    29. 

  29. JTT rate matrix prepared using the DCMut method*

    30. 

  30. ------------------------------------------------

    31. 

  31. 

    32. 

  32. The first part above indicates the symmetric 'exchangeability' parameters s_ij, 

    33. 

  33. where s_ij = s_ji.

    34. 

  34. The second part gives the amino acid equilibrium frequencies pi_i. 

    35. 

  35. The net replacement rate from i to j is q_ij = pi_j*s_ij.

    36. 

  36.         

    37. 

  37. This model is usually scaled so that the mean rate of change at

    38. 

  38. equilibrium, Sum_i Sum_j!=i pi_i*q_ij, equals 1.  You should check this

    39. 

  39. scaling before using the matrix above.  The PAML package will perform

    40. 

  40. this scaling.

    41. 

  41. 

    42. 

  42. //

    43. 

  43. 

    44. 

  44. *Prepared by Carolin Kosiol and Nick Goldman, December 2003.

    45. 

  45. 

    46. 

  46. See the following paper for more details:

    47. 

  47. Kosiol, C., and Goldman, N. 2005. Different versions of the Dayhoff rate matrix. 

    48. 

  48. Molecular Biology and Evolution 22:193-199.

    49. 

  49. 

    50. 

  50. See also http://www.ebi.ac.uk/goldman/dayhoff
    51.