/usr/share/phast/data/exoniphy/mammals/hky.start-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: 0.000000 0.000000 0.000000 1.000000
RATE_MAT:
0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
TREE: (human:0.000000,(mouse:0.000000,rat:0.000000):0.000000);
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