/usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-1.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 | ALPHABET: A C G T
ORDER: 0
SUBST_MOD: HKY85
BACKGROUND: 0.340794 0.357356 0.183896 0.117954
RATE_MAT:
-0.906618 0.278388 0.536340 0.091889
0.265487 -0.752765 0.143259 0.344019
0.993943 0.278388 -1.364220 0.091889
0.265487 1.042244 0.143259 -1.450990
TREE: (human:0.041041,(mouse:0.016993,rat:0.017579):0.041041);
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