/PAMLdat/dayhoff.dat
http://github.com/sbotond/phylosim · Unknown · 132 lines · 103 code · 29 blank · 0 comment · 0 complexity · f6839f30ef8ef1951d6f8c31ca554aa4 MD5 · raw file
- 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)
- ----------------------------------------------------------------
-
-
-
- Some notes from 1995, for those technical people:
-
- I managed to find some notes I wrote in 1995. The symbols are not
- that comprehensible now, but you can get the basic idea, I think.
-
- (1) Construction of P(0.01), for 1 PAM
- p_ij(0.01) = m_i * A_{ij}/\sum_k{A_{ik}} / 7524.6
-
- (2) Eigensolution of P(0.01) = exp{Q*0.01}
- P(0.01) = U diag{\lambda...} U^{-1}
-
- Then
- Q = U diag{100*log{\lambda}...} U^{-1}
-
-
- I did not use the PAM transition probabilities as rates assuming 0.01
- is close to 0, but instead take them as P(0.01) to recover the rate
- matrix, and as we expect, the rates are more different from each other
- than the p_ij(0.01) are.
-
- I seem to recall that I thought some details in the Dayhoff paper and
- the Kishino et al. (1990) paper were not entirely right. I think I
- thought that Q should be a symmetrical matrix, right-multiplied by a
- diagonal matrix, while either Dayhoff or Kishino or both used
- left-multiplication.
-
- As far as I know, codeml and protml give very similar (but not
- identical, I think) results under the Dayhoff model.
-
- My jones.dat file is not based on the Jones et al. (1992) paper, but
- is based on an updated data set sent to me by David Jones. So codeml
- and protml gave different results under JTT, but ranking of trees was
- not affected for the data set I tested.
-
- Ziheng Yang