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/PAMLdat/dayhoff.dat

http://github.com/sbotond/phylosim
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  1      
  2 27									    
  3 98  32									    
  4120   0 905								    
  5 36  23   0   0								    
  6 89 246 103 134   0							    
  7198   1 148 1153  0 716							    
  8240   9 139 125  11  28  81						    
  9 23 240 535  86  28 606  43  10						    
 10 65  64  77  24  44  18  61   0   7					    
 11 41  15  34   0   0  73  11   7  44 257					    
 12 26 464 318  71   0 153  83  27  26  46  18				    
 13 72  90   1   0   0 114  30  17   0 336 527 243				    
 14 18  14  14   0   0   0   0  15  48 196 157   0  92			    
 15250 103  42  13  19 153  51  34  94  12  32  33  17  11			    
 16409 154 495  95 161  56  79 234  35  24  17  96  62  46 245		    
 17371  26 229  66  16  53  34  30  22 192  33 136 104  13  78 550		    
 18  0 201  23   0   0   0   0   0  27   0  46   0   0  76   0  75   0	    
 19 24   8  95   0  96   0  22   0 127  37  28  13   0 698   0  34  42  61	    
 20208  24  15  18  49  35  37  54  44 889 175  10 258  12  48  30 157   0  28 
 21
 220.087127 0.040904 0.040432 0.046872 0.033474 0.038255 0.049530
 230.088612 0.033618 0.036886 0.085357 0.080482 0.014753 0.039772
 240.050680 0.069577 0.058542 0.010494 0.029916 0.064718
 25
 26Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
 27
 28S_ij = S_ji and PI_i for the Dayhoff model, with the rate Q_ij=S_ij*PI_j
 29The rest of the file is not used.
 30Prepared by Z. Yang, March 1995.
 31
 32
 33See the following reference for notation used here:
 34
 35Yang, Z., R. Nielsen and M. Hasegawa. 1998. Models of amino acid substitution and
 36applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611.
 37
 38
 39-----------------------------------------------------------------------
 40
 41     
 42 30									   
 43109  17									   
 44154   0 532								   
 45 33  10   0   0 							   
 46 93 120  50  76   0							   
 47266   0  94 831   0 422							   
 48579  10 156 162  10  30 112						   
 49 21 103 226  43  10 243  23  10 					   
 50 66  30  36  13  17   8  35   0   3					   
 51 95  17  37   0   0  75  15  17  40 253					   
 52 57 477 322  85   0 147 104  60  23  43  39				   
 53 29  17   0   0   0  20   7   7   0  57 207  90				   
 54 20   7   7   0   0   0   0  17  20  90 167   0  17 			   
 55345  67  27  10  10  93  40  49  50   7  43  43   4   7			   
 56772 137 432  98 117  47  86 450  26  20  32 168  20  40 269		   
 57590  20 169  57  10  37  31  50  14 129  52 200  28  10  73 696		   
 58  0  27   3   0   0   0   0   0   3   0  13   0   0  10   0  17  0	   
 59 20   3  36   0  30   0  10   0  40  13  23  10   0 260   0  22  23  6	   
 60365  20  13  17  33  27  37  97  30 661 303  17  77  10  50  43 186  0  17  
 61 A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y  V
 62Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
 63
 64Accepted point mutations (x10) Figure 80 (Dayhoff 1978)
 65-------------------------------------------------------
 66
 67A 100 /* Ala */		    A 0.087 /* Ala */
 68R  65 /* Arg */		    R 0.041 /* Arg */
 69N 134 /* Asn */		    N 0.040 /* Asn */
 70D 106 /* Asp */		    D 0.047 /* Asp */
 71C  20 /* Cys */		    C 0.033 /* Cys */
 72Q  93 /* Gln */		    Q 0.038 /* Gln */
 73E 102 /* Glu */		    E 0.050 /* Glu */
 74G  49 /* Gly */             G 0.089 /* Gly */
 75H  66 /* His */		    H 0.034 /* His */
 76I  96 /* Ile */		    I 0.037 /* Ile */
 77L  40 /* Leu */		    L 0.085 /* Leu */
 78K  56 /* Lys */		    K 0.081 /* Lys */
 79M  94 /* Met */		    M 0.015 /* Met */
 80F  41 /* Phe */		    F 0.040 /* Phe */
 81P  56 /* Pro */		    P 0.051 /* Pro */
 82S 120 /* Ser */		    S 0.070 /* Ser */
 83T  97 /* Thr */		    T 0.058 /* Thr */
 84W  18 /* Trp */		    W 0.010 /* Trp */
 85Y  41 /* Tyr */		    Y 0.030 /* Tyr */
 86V  74 /* Val */		    V 0.065 /* Val */
 87
 88scale factor = SUM_OF_PRODUCT = 75.246
 89
 90
 91Relative Mutability         The equilibrium freqs.
 92(Table 21)		    Table 22    
 93(Dayhoff 1978)		    Dayhoff (1978)        
 94----------------------------------------------------------------
 95
 96
 97
 98Some notes from 1995, for those technical people:
 99
100I managed to find some notes I wrote in 1995.  The symbols are not
101that comprehensible now, but you can get the basic idea, I think.  
102
103(1) Construction of P(0.01), for 1 PAM
104    p_ij(0.01) = m_i * A_{ij}/\sum_k{A_{ik}} / 7524.6
105
106(2) Eigensolution of P(0.01) = exp{Q*0.01}
107    P(0.01) = U diag{\lambda...} U^{-1}
108
109    Then 
110    Q = U diag{100*log{\lambda}...} U^{-1}
111
112
113I did not use the PAM transition probabilities as rates assuming 0.01
114is close to 0, but instead take them as P(0.01) to recover the rate
115matrix, and as we expect, the rates are more different from each other
116than the p_ij(0.01) are.
117
118I seem to recall that I thought some details in the Dayhoff paper and
119the Kishino et al. (1990) paper were not entirely right.  I think I
120thought that Q should be a symmetrical matrix, right-multiplied by a
121diagonal matrix, while either Dayhoff or Kishino or both used
122left-multiplication.
123
124As far as I know, codeml and protml give very similar (but not
125identical, I think) results under the Dayhoff model.
126
127My jones.dat file is not based on the Jones et al. (1992) paper, but
128is based on an updated data set sent to me by David Jones.  So codeml
129and protml gave different results under JTT, but ranking of trees was
130not affected for the data set I tested.
131
132Ziheng Yang