/usr/share/phast/data/exoniphy/mammals/hky.stop-3.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: 0.776401 0.000000 0.223599 0.000000
RATE_MAT:
-0.643997 0.000000 0.643997 0.000000
1.178327 -1.517677 0.339350 0.000000
2.236151 0.000000 -2.236151 0.000000
1.178327 0.000000 0.339350 -1.517677
TREE: (human:0.033173,(mouse:0.012677,rat:0.013123):0.033173);
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