/usr/include/libphylo/dayhoff.dat.q is in rate4site 3.0.0-5.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 | " 27 "
" 98 32 "
" 120 0 905 "
" 36 23 0 0 "
" 89 246 103 134 0 "
" 198 1 148 1153 0 716 "
" 240 9 139 125 11 28 81 "
" 23 240 535 86 28 606 43 10 "
" 65 64 77 24 44 18 61 0 7 "
" 41 15 34 0 0 73 11 7 44 257 "
" 26 464 318 71 0 153 83 27 26 46 18 "
" 72 90 1 0 0 114 30 17 0 336 527 243 "
" 18 14 14 0 0 0 0 15 48 196 157 0 92 "
" 250 103 42 13 19 153 51 34 94 12 32 33 17 11 "
" 409 154 495 95 161 56 79 234 35 24 17 96 62 46 245 "
" 371 26 229 66 16 53 34 30 22 192 33 136 104 13 78 550 "
" 0 201 23 0 0 0 0 0 27 0 46 0 0 76 0 75 0 "
" 24 8 95 0 96 0 22 0 127 37 28 13 0 698 0 34 42 61 "
" 208 24 15 18 49 35 37 54 44 889 175 10 258 12 48 30 157 0 28 "
" 0.087127 0.040904 0.040432 0.046872 0.033474 0.038255 0.049530 "
" 0.088612 0.033618 0.036886 0.085357 0.080482 0.014753 0.039772 "
" 0.050680 0.069577 0.058542 0.010494 0.029916 0.064718 "
" Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val "
" S_ij = S_ji and PI_i for the Dayhoff model, with the rate Q_ij=S_ij*PI_j "
" The rest of the file is not used. "
" Prepared by Z. Yang, March 1995. "
" See the following reference for notation used here: "
" Yang, Z., R. Nielsen and M. Hasegawa. 1998. Models of amino acid substitution and "
" applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611. "
" ----------------------------------------------------------------------- "
" "
" 30 "
" 109 17 "
" 154 0 532 "
" 33 10 0 0 "
" 93 120 50 76 0 "
" 266 0 94 831 0 422 "
" 579 10 156 162 10 30 112 "
" 21 103 226 43 10 243 23 10 "
" 66 30 36 13 17 8 35 0 3 "
" 95 17 37 0 0 75 15 17 40 253 "
" 57 477 322 85 0 147 104 60 23 43 39 "
" 29 17 0 0 0 20 7 7 0 57 207 90 "
" 20 7 7 0 0 0 0 17 20 90 167 0 17 "
" 345 67 27 10 10 93 40 49 50 7 43 43 4 7 "
" 772 137 432 98 117 47 86 450 26 20 32 168 20 40 269 "
" 590 20 169 57 10 37 31 50 14 129 52 200 28 10 73 696 "
" 0 27 3 0 0 0 0 0 3 0 13 0 0 10 0 17 0 "
" 20 3 36 0 30 0 10 0 40 13 23 10 0 260 0 22 23 6 "
" 365 20 13 17 33 27 37 97 30 661 303 17 77 10 50 43 186 0 17 "
" A R N D C Q E G H I L K M F P S T W Y V "
" Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val "
" Accepted point mutations (x10) Figure 80 (Dayhoff 1978) "
" ------------------------------------------------------- "
" A 100 /* Ala */ A 0.087 /* Ala */ "
" R 65 /* Arg */ R 0.041 /* Arg */ "
" N 134 /* Asn */ N 0.040 /* Asn */ "
" D 106 /* Asp */ D 0.047 /* Asp */ "
" C 20 /* Cys */ C 0.033 /* Cys */ "
" Q 93 /* Gln */ Q 0.038 /* Gln */ "
" E 102 /* Glu */ E 0.050 /* Glu */ "
" G 49 /* Gly */ G 0.089 /* Gly */ "
" H 66 /* His */ H 0.034 /* His */ "
" I 96 /* Ile */ I 0.037 /* Ile */ "
" L 40 /* Leu */ L 0.085 /* Leu */ "
" K 56 /* Lys */ K 0.081 /* Lys */ "
" M 94 /* Met */ M 0.015 /* Met */ "
" F 41 /* Phe */ F 0.040 /* Phe */ "
" P 56 /* Pro */ P 0.051 /* Pro */ "
" S 120 /* Ser */ S 0.070 /* Ser */ "
" T 97 /* Thr */ T 0.058 /* Thr */ "
" W 18 /* Trp */ W 0.010 /* Trp */ "
" Y 41 /* Tyr */ Y 0.030 /* Tyr */ "
" V 74 /* Val */ V 0.065 /* Val */ "
" scale factor = SUM_OF_PRODUCT = 75.246 "
" Relative Mutability The equilibrium freqs. "
" (Table 21) Table 22 "
" (Dayhoff 1978) Dayhoff (1978) "
" ---------------------------------------------------------------- "
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