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