/usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc5.mod is in phast 1.4+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | ALPHABET: A C G T
ORDER: 2
SUBST_MOD: R3
NRATECATS: 4
ALPHA: 1.989657
BACKGROUND: 0.011522 0.020584 0.032272 0.009179 0.012003 0.021979 0.007724 0.009250 0.006225 0.023039 0.010349 0.008820 0.003330 0.025741 0.018208 0.009014 0.006432 0.018348 0.037859 0.007406 0.014797 0.024228 0.008851 0.016672 0.006719 0.016720 0.016354 0.006208 0.006406 0.023551 0.058049 0.009011 0.017010 0.032814 0.048778 0.016254 0.014224 0.038261 0.010146 0.018386 0.013275 0.031033 0.019272 0.011649 0.005086 0.017799 0.038459 0.006299 0.000000 0.018061 0.000000 0.008444 0.007971 0.018837 0.005416 0.010461 0.000000 0.014283 0.013372 0.008024 0.002773 0.024785 0.010080 0.011899
RATE_MAT:
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TREE: (human:0.139887,(mouse:0.034951,rat:0.034973):0.139887);
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