/usr/include/libphylo/jones.dat.q is in rate4site 3.0.0-2.
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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 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 | " 58 "
" 54 45 "
" 81 16 528 "
" 56 113 34 10 "
" 57 310 86 49 9 "
" 105 29 58 767 5 323 "
" 179 137 81 130 59 26 119 "
" 27 328 391 112 69 597 26 23 "
" 36 22 47 11 17 9 12 6 16 "
" 30 38 12 7 23 72 9 6 56 229 "
" 35 646 263 26 7 292 181 27 45 21 14 "
" 54 44 30 15 31 43 18 14 33 479 388 65 "
" 15 5 10 4 78 4 5 5 40 89 248 4 43 "
" 194 74 15 15 14 164 18 24 115 10 102 21 16 17 "
" 378 101 503 59 223 53 30 201 73 40 59 47 29 92 285 "
" 475 64 232 38 42 51 32 33 46 245 25 103 226 12 118 477 "
" 9 126 8 4 115 18 10 55 8 9 52 10 24 53 6 35 12 "
" 11 20 70 46 209 24 7 8 573 32 24 8 18 536 10 63 21 71 "
" 298 17 16 31 62 20 45 47 11 961 180 14 323 62 23 38 112 25 16 "
" 0.076748 0.051691 0.042645 0.051544 0.019803 0.040752 0.061830 "
" 0.073152 0.022944 0.053761 0.091904 0.058676 0.023826 0.040126 "
" 0.050901 0.068765 0.058565 0.014261 0.032102 0.066005 "
" 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 Jones model based on the SWISSPROT "
" Version 22 data. "
" 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: "
" 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. "
" ----------------------------------------------------------------------- "
" 426 "
" 333 185 "
" 596 80 2134 "
" 159 214 54 20 "
" 332 1203 277 192 14 "
" 920 176 286 4497 11 1497 "
" 1853 954 470 907 158 144 999 "
" 88 716 704 244 58 1027 69 71 "
" 286 114 198 59 34 37 72 44 37 "
" 394 332 88 62 79 497 101 80 217 2086 "
" 294 3606 1209 148 15 1289 1210 215 115 121 140 "
" 185 100 56 34 27 78 50 47 33 1129 1567 167 "
" 84 21 33 16 115 14 23 28 69 354 1690 17 76 "
" 1395 360 64 74 27 629 106 171 249 54 882 117 36 66 "
" 3664 661 2706 390 559 278 236 1861 214 274 691 351 89 468 1839 "
" 3920 360 1069 216 91 227 217 266 116 1420 256 653 579 54 653 3527 "
" 19 171 9 5 60 20 17 106 5 13 127 16 15 56 8 64 18 "
" 49 62 178 142 246 59 26 34 777 102 131 30 25 1276 32 259 73 60 "
" 2771 111 86 195 150 100 336 420 32 6260 2020 99 937 307 142 320 805 44 63 "
" 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), similar to Figure 80 of Dayhoff et "
" al. (1978). SwissProt version 22 data. "
" ------------------------------------------------------------------------------ "
" 256458 426 333 596 159 332 920 1853 88 286 394 294 185 84 1395 3664 3920 19 49 2771 "
" 426 182302 185 80 214 1203 176 954 716 114 332 3606 100 21 360 661 360 171 62 111 "
" 333 185 150772 2134 54 277 286 470 704 198 88 1209 56 33 64 2706 1069 9 178 86 "
" 596 80 2134 178390 20 192 4497 907 244 59 62 148 34 16 74 390 216 5 142 195 "
" 159 214 54 20 68120 14 11 158 58 34 79 15 27 115 27 559 91 60 246 150 "
" 332 1203 277 192 14 139546 1497 144 1027 37 497 1289 78 14 629 278 227 20 59 100 "
" 920 176 286 4497 11 1497 218432 999 69 72 101 1210 50 23 106 236 217 17 26 336 "
" 1853 954 470 907 158 144 999 255274 71 44 80 215 47 28 171 1861 266 106 34 420 "
" 88 716 704 244 58 1027 69 71 77124 37 217 115 33 69 249 214 116 5 777 32 "
" 286 114 198 59 34 37 72 44 37 191018 2086 121 1129 354 54 274 1420 13 102 6260 "
" 394 332 88 62 79 497 101 80 217 2086 319504 140 1567 1690 882 691 256 127 131 2020 "
" 294 3606 1209 148 15 1289 1210 215 115 121 140 206568 167 17 117 351 653 16 30 99 "
" 185 100 56 34 27 78 50 47 33 1129 1567 167 84670 76 36 89 579 15 25 937 "
" 84 21 33 16 115 14 23 28 69 354 1690 17 76 143088 66 468 54 56 1276 307 "
" 1395 360 64 74 27 629 106 171 249 54 882 117 36 66 175488 1839 653 8 32 142 "
" 3664 661 2706 390 559 278 236 1861 214 274 691 351 89 468 1839 234536 3527 64 259 320 "
" 3920 360 1069 216 91 227 217 266 116 1420 256 653 579 54 653 3527 203636 18 73 805 "
" 19 171 9 5 60 20 17 106 5 13 127 16 15 56 8 64 18 50486 60 44 "
" 49 62 178 142 246 59 26 34 777 102 131 30 25 1276 32 259 73 60 114728 63 "
" 2771 111 86 195 150 100 336 420 32 6260 2020 99 937 307 142 320 805 44 63 223724 "
" Observed difference counts from pairwise comparisons, with ancestral sequences "
" constructed by parsimony. F(t) = PI*P(t). "
" Based on the SwissProt 22 data, kindly provided by D. Jones (Jones et al. 1992) "
" ------------------------------------------------------------------------------- "
" Ala 0.98754 0.00030 0.00023 0.00042 0.00011 0.00023 0.00065 0.00130 0.00006 0.00020 0.00028 0.00021 0.00013 0.00006 0.00098 0.00257 0.00275 0.00001 0.00003 0.00194 "
" Arg 0.00044 0.98974 0.00019 0.00008 0.00022 0.00125 0.00018 0.00099 0.00075 0.00012 0.00035 0.00376 0.00010 0.00002 0.00037 0.00069 0.00037 0.00018 0.00006 0.00012 "
" Asn 0.00042 0.00023 0.98720 0.00269 0.00007 0.00035 0.00036 0.00059 0.00089 0.00025 0.00011 0.00153 0.00007 0.00004 0.00008 0.00342 0.00135 0.00001 0.00022 0.00011 "
" Asp 0.00062 0.00008 0.00223 0.98954 0.00002 0.00020 0.00470 0.00095 0.00025 0.00006 0.00006 0.00015 0.00004 0.00002 0.00008 0.00041 0.00023 0.00001 0.00015 0.00020 "
" Cys 0.00043 0.00058 0.00015 0.00005 0.99432 0.00004 0.00003 0.00043 0.00016 0.00009 0.00021 0.00004 0.00007 0.00031 0.00007 0.00152 0.00025 0.00016 0.00067 0.00041 "
" Gln 0.00044 0.00159 0.00037 0.00025 0.00002 0.98955 0.00198 0.00019 0.00136 0.00005 0.00066 0.00170 0.00010 0.00002 0.00083 0.00037 0.00030 0.00003 0.00008 0.00013 "
" Glu 0.00080 0.00015 0.00025 0.00392 0.00001 0.00130 0.99055 0.00087 0.00006 0.00006 0.00009 0.00105 0.00004 0.00002 0.00009 0.00021 0.00019 0.00001 0.00002 0.00029 "
" Gly 0.00136 0.00070 0.00035 0.00067 0.00012 0.00011 0.00074 0.99350 0.00005 0.00003 0.00006 0.00016 0.00003 0.00002 0.00013 0.00137 0.00020 0.00008 0.00003 0.00031 "
" His 0.00021 0.00168 0.00165 0.00057 0.00014 0.00241 0.00016 0.00017 0.98864 0.00009 0.00051 0.00027 0.00008 0.00016 0.00058 0.00050 0.00027 0.00001 0.00182 0.00008 "
" Ile 0.00029 0.00011 0.00020 0.00006 0.00003 0.00004 0.00007 0.00004 0.00004 0.98729 0.00209 0.00012 0.00113 0.00035 0.00005 0.00027 0.00142 0.00001 0.00010 0.00627 "
" Leu 0.00023 0.00019 0.00005 0.00004 0.00005 0.00029 0.00006 0.00005 0.00013 0.00122 0.99330 0.00008 0.00092 0.00099 0.00052 0.00040 0.00015 0.00007 0.00008 0.00118 "
" Lys 0.00027 0.00331 0.00111 0.00014 0.00001 0.00118 0.00111 0.00020 0.00011 0.00011 0.00013 0.99100 0.00015 0.00002 0.00011 0.00032 0.00060 0.00001 0.00003 0.00009 "
" Met 0.00042 0.00023 0.00013 0.00008 0.00006 0.00018 0.00011 0.00011 0.00007 0.00255 0.00354 0.00038 0.98818 0.00017 0.00008 0.00020 0.00131 0.00003 0.00006 0.00212 "
" Phe 0.00011 0.00003 0.00004 0.00002 0.00015 0.00002 0.00003 0.00004 0.00009 0.00047 0.00227 0.00002 0.00010 0.99360 0.00009 0.00063 0.00007 0.00008 0.00171 0.00041 "
" Pro 0.00148 0.00038 0.00007 0.00008 0.00003 0.00067 0.00011 0.00018 0.00026 0.00006 0.00093 0.00012 0.00004 0.00007 0.99270 0.00194 0.00069 0.00001 0.00003 0.00015 "
" Ser 0.00287 0.00052 0.00212 0.00031 0.00044 0.00022 0.00018 0.00146 0.00017 0.00021 0.00054 0.00027 0.00007 0.00037 0.00144 0.98556 0.00276 0.00005 0.00020 0.00025 "
" Thr 0.00360 0.00033 0.00098 0.00020 0.00008 0.00021 0.00020 0.00024 0.00011 0.00131 0.00024 0.00060 0.00053 0.00005 0.00060 0.00324 0.98665 0.00002 0.00007 0.00074 "
" Trp 0.00007 0.00065 0.00003 0.00002 0.00023 0.00008 0.00006 0.00040 0.00002 0.00005 0.00048 0.00006 0.00006 0.00021 0.00003 0.00024 0.00007 0.99686 0.00023 0.00017 "
" Tyr 0.00008 0.00010 0.00030 0.00024 0.00041 0.00010 0.00004 0.00006 0.00130 0.00017 0.00022 0.00005 0.00004 0.00214 0.00005 0.00043 0.00012 0.00010 0.99392 0.00011 "
" Val 0.00226 0.00009 0.00007 0.00016 0.00012 0.00008 0.00027 0.00034 0.00003 0.00511 0.00165 0.00008 0.00076 0.00025 0.00012 0.00026 0.00066 0.00004 0.00005 0.98761 "
" P(0.01), amino acid exchange data generated from SWISSPROT Release 22.0 "
" Ref. Jones D.T., Taylor W.R. and Thornton J.M. (1992) CABIOS 8:275-282 "
" Usable sequences: 23824 "
" Final alignments: 5437 "
" Accepted point mutations: 92883 "
" A R N D C Q E G H I L K M F P S T W Y V "
" 0.0767477 100 "
" 0.0516907 82.3263 "
" 0.0426448 102.697 "
" 0.0515445 83.8924 "
" 0.0198027 45.6097 "
" 0.0407523 83.8825 "
" 0.0618296 75.7914 "
" 0.0731516 52.1273 "
" 0.0229438 91.1374 "
" 0.0537609 101.99 "
" 0.0919042 53.7672 "
" 0.0586762 72.2308 "
" 0.0238262 94.8144 "
" 0.0401265 51.3146 "
" 0.0509007 58.5874 "
" 0.0687652 115.899 "
" 0.0585647 107.092 "
" 0.0142613 25.2297 "
" 0.0321015 48.7629 "
" 0.0660051 99.4571 "
" "
" Normalized Relative "
" frequency mutabilities "
" (SUM m*f) = 80.240436 "
" ------------------------------------------- "
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