/usr/include/libphylo/adrianCodon.dat.q is in rate4site 3.0.0-2.
This file is owned by root:root, with mode 0o644.
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" 0 140 1656 380 71026 41523 "
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" 328 7142 272 370 715 4680 1286 876 707 "
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" 607 43 47 105 5067 0 0 0 863 56 221 189 "
" 0 301 43 0 0 2141 279 0 0 475 32 0 27331 "
" 167 88 393 141 1487 366 3364 545 193 140 538 162 5087 1030 "
" 34 0 42 421 0 0 346 3233 0 0 61 718 31469 35230 1626 "
" 2841 308 69 647 711 76 0 346 1297 278 124 413 193 49 200 0 "
" 195 2491 229 114 57 356 73 12 114 945 197 0 8 74 42 9 2449 "
" 286 295 1514 350 199 128 640 63 66 257 565 175 42 15 241 41 31892 2201 "
" 352 19 175 3379 195 32 0 441 246 85 129 1259 106 0 126 176 4155 62775 2262 "
" 190 36 58 114 2112 0 0 0 0 51 81 158 201 0 114 51 2926 203 490 116 "
" 37 204 30 71 0 1701 355 109 35 444 1 0 27 114 56 21 205 1284 335 79 21842 "
" 81 99 218 95 183 0 4067 30 94 182 10 76 164 61 192 0 617 512 2569 361 57041 44793 "
" 54 30 30 239 134 158 0 2062 10 30 35 370 101 0 70 141 263 0 183 1574 32490 33996 32457 "
" 1891 0 623 93 0 147 671 0 46674 151 12628 0 11 0 0 134 8237 543 0 277 818 47 0 0 "
" 701 549 1184 0 0 246 241 87 5836 1540 12311 0 6 41 48 0 452 5598 739 0 16 841 253 0 40388 "
" 854 120 2602 57 54 69 359 0 13337 47 37725 91 0 31 105 0 0 660 5014 399 118 0 2656 0 82443 40802 "
" 695 0 735 893 81 28 0 661 12916 0 6008 2384 89 35 60 56 1344 0 484 9142 0 0 0 1483 85032 87710 53112 "
" 208 39 0 46 600 0 0 0 19 0 0 55 7884 0 1512 386 2427 200 95 0 3069 0 0 0 2011 0 15 0 "
" 35 133 6 0 0 387 59 0 0 142 42 0 365 3634 769 272 79 813 191 114 0 1470 0 70 95 1012 0 0 17551 "
" 0 15 74 0 97 91 378 52 27 44 46 8 876 732 2298 588 106 83 604 90 286 0 1947 0 0 70 707 0 33878 14863 "
" 63 0 14 229 8 0 114 484 67 48 0 147 280 278 720 3849 349 0 160 1407 0 0 0 1951 0 3 43 1427 22703 32337 15002 "
" 1304 155 0 389 408 75 0 79 444 170 0 236 197 11 45 0 2595 59 234 256 149 35 74 60 51 0 0 143 109 12 0 27 "
" 120 2602 73 69 0 258 160 112 46 821 22 78 0 43 18 0 158 647 151 46 14 149 84 17 1 119 23 2 0 42 7 20 2320 "
" 0 168 893 221 158 73 415 109 0 180 336 209 35 1 131 44 138 148 1538 143 107 83 168 39 1 91 217 0 0 26 55 14 23280 3052 "
" 117 9 91 3406 173 5 0 311 55 62 40 1017 39 0 16 75 274 0 113 787 57 14 76 93 0 16 26 138 10 0 1 44 3660 28072 2533 "
" 450 59 100 310 7741 0 0 0 225 220 182 557 1008 0 588 153 639 41 127 145 2469 39 211 190 150 0 48 78 625 0 97 61 1324 82 245 122 "
" 28 466 94 52 0 6013 75 0 50 1265 106 0 0 452 240 0 47 248 183 0 14 2010 303 164 55 277 0 61 0 333 64 62 86 670 189 0 17008 "
" 130 336 356 168 0 401 16072 0 103 537 357 370 656 161 817 0 379 93 512 228 0 428 10166 0 0 195 789 0 0 83 543 33 0 379 1907 42 47381 29661 "
" 89 80 65 525 0 0 0 7268 98 211 0 1307 86 67 226 484 125 11 108 230 58 130 0 2312 0 0 130 252 29 17 64 381 133 0 145 799 30850 26704 28871 "
" 285 65 23 253 446 24 106 6 2230 278 0 315 177 0 65 33 468 34 17 54 163 23 55 33 366 0 0 0 145 26 0 28 1661 180 0 104 2231 92 0 278 "
" 28 1227 58 189 12 521 129 103 53 5470 0 0 37 87 33 21 31 344 83 26 64 236 268 30 0 941 162 1 0 80 13 28 0 1655 105 0 0 2186 744 149 19297 "
" 27 356 299 139 176 0 843 160 0 684 3262 829 29 45 241 0 110 65 309 60 76 115 522 18 0 0 1073 0 0 2 82 0 0 67 1559 183 750 315 5134 73 44365 23295 "
" 92 205 66 1727 96 190 0 728 0 13 0 7147 0 0 47 96 0 0 89 555 60 34 0 335 244 0 0 1432 18 0 18 105 59 0 63 2203 356 0 0 2632 28434 37047 23095 "
" 318 54 33 115 3527 41 76 0 518 181 0 64 23970 0 1303 260 576 75 64 47 821 131 0 0 179 0 0 0 4505 11 14 274 764 39 80 51 6746 0 0 30 1310 0 179 0 "
" 27 179 23 44 3 2249 0 308 11 354 78 34 330 12669 395 164 61 157 53 32 75 413 144 0 0 108 75 38 251 3338 87 38 51 294 54 0 0 4666 0 0 0 797 0 0 22326 "
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" 76 42 6 207 135 150 294 2554 64 143 0 486 810 110 539 13791 171 2 57 142 0 0 134 537 0 31 5 200 0 58 22 3459 129 0 7 388 0 0 0 5346 0 31 0 1160 31707 35610 22203 "
" 18 407 23 0 0 68 19 36 42 165 0 0 2 88 44 2 117 3381 122 0 0 99 45 6 0 290 36 0 0 266 30 38 18 159 13 0 1 58 142 23 0 80 5 0 3 144 35 0 "
" 33 0 23 658 24 44 108 126 0 20 64 327 60 14 66 133 254 286 87 4548 15 0 8 90 141 9 0 754 142 1 81 288 33 0 33 255 39 24 0 112 18 0 29 130 37 14 20 166 53555 "
" 277 164 108 290 6514 235 482 1018 165 446 8 1100 435 12 319 0 838 111 227 157 5890 0 507 0 340 0 64 3 320 0 0 0 245 73 90 109 6631 419 0 627 412 59 338 125 825 102 176 201 47 59 "
" 51 577 50 66 169 4821 1421 355 54 2047 24 106 112 72 80 62 188 439 166 46 0 5279 0 0 0 368 104 23 0 445 72 0 30 239 87 0 264 4869 738 374 122 466 103 38 4 415 40 126 541 37 22923 "
" 110 82 145 163 1203 0 14459 754 24 1451 151 763 183 30 477 38 0 233 599 0 273 0 12183 0 111 219 802 0 707 0 0 0 110 158 176 42 520 675 20335 0 0 499 1107 178 0 0 564 0 146 0 76141 40261 "
" 112 181 54 602 1180 581 0 5578 112 651 68 1954 0 31 157 150 297 90 115 657 0 135 0 5714 0 0 0 679 0 0 41 578 87 3 74 288 631 521 937 5109 167 107 21 611 147 31 96 454 0 834 31553 32600 44414 "
" 31 241 33 0 45 319 0 86 16 1649 42 219 33 130 46 2 125 576 73 12 0 102 64 24 110 1890 226 0 0 317 18 43 0 51 24 0 56 410 279 66 0 774 82 0 50 219 33 124 1297 0 172 1595 327 77 "
" 20 14 49 22 39 18 92 0 48 39 549 56 30 14 95 20 79 42 201 130 28 0 142 1 270 84 1199 29 74 19 105 19 10 3 27 6 35 31 67 0 8 14 446 0 13 9 56 41 166 229 174 47 576 33 341 "
" 43 8 28 397 156 20 280 403 108 352 75 2043 29 21 59 187 145 43 89 989 22 0 91 211 106 0 104 2711 123 20 35 305 27 19 7 86 180 46 200 423 72 80 88 1072 108 58 112 224 0 2135 495 0 187 2090 61046 387 "
" 123 9 9 101 615 6 102 140 180 69 106 0 6752 231 1116 418 193 9 104 167 205 38 23 15 0 83 4 103 54777 7485 8703 8464 67 34 41 0 611 88 0 90 49 0 18 92 6666 153 0 364 159 265 4644 80 0 186 96 51 168 "
" 12 70 0 0 23 155 11 48 3 70 0 0 70 742 186 61 38 346 27 46 25 170 6 0 0 117 17 14 220 2693 284 0 5 27 8 0 0 162 124 20 3 48 23 0 28 957 87 0 3979 750 23 924 0 0 574 154 61 1268 "
" 59 45 80 75 192 81 637 163 28 0 74 99 1733 57 3345 832 131 42 198 55 181 6 226 149 53 0 94 204 14044 5603 27723 9664 97 0 37 34 172 50 1000 141 1 32 254 0 523 72 2117 491 102 84 1377 107 5207 276 111 744 201 47609 814 "
" 9 17 12 85 47 14 107 170 21 21 26 101 326 48 262 910 73 74 23 359 0 0 55 201 17 0 20 146 234 0 387 2714 16 0 5 30 82 2 39 186 30 18 5 66 172 13 125 928 625 4904 160 0 206 991 125 212 787 1638 32469 1494 "
" 0.0282483 0.0206292 0.0319075 0.0182494 0.0168831 0.0159757 0.0058938 0.0144022 0.0135116 0.0190724 0.0118542 0.0136325 0.0093705 0.0199714 0.0218874 0.0174818 "
" 0.0136792 0.0143825 0.0337043 0.0116006 0.0177685 0.0150006 0.0058835 0.0176118 0.0061893 0.0087184 0.0084944 0.0054224 0.0080368 0.0173529 0.0373569 0.0150280 "
" 0.0311168 0.0246045 0.0388972 0.0251865 0.0179100 0.0212765 0.0059683 0.0199671 0.0184506 0.0176209 0.0132786 0.0115579 0.0083782 0.0137699 0.0265260 0.0136025 "
" 0.0159995 0.0132055 0.0133496 0.0159777 0.0043280 0.0171276 0.0119089 0.0124708 0.0109899 0.0085271 0.0195872 0.0141357 0.0190797 "
" AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT "
" CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT "
" GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT "
" TAC TAT TCA TCC TCG TCT TGC TGG TGT TTA TTC TTG TTT "
" S_ij = S_ji and PI_i based on the empirical codon matrix: "
" A Schneider, GM Cannarozzi and GH Gonnet. Empirical codon "
" substitution matrix. BMC Bioinformatics 6:134. 2005. "
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