/usr/share/phast/data/exoniphy/mammals/hky.stop-2.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: 0.487073 0.000000 0.512927 0.000000
RATE_MAT:
-1.026541 0.000000 1.026541 0.000000
0.290945 -0.597333 0.306388 0.000000
0.974797 0.000000 -0.974797 0.000000
0.290945 0.000000 0.306388 -0.597333
TREE: (human:0.045836,(mouse:0.016398,rat:0.017577):0.045836);
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