/usr/share/phast/data/exoniphy/mammals/hky.prestart-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: 0.487058 0.083651 0.381678 0.047614
RATE_MAT:
-0.954405 0.043240 0.886553 0.024612
0.251766 -0.559656 0.197294 0.110596
1.131329 0.043240 -1.199181 0.024612
0.251766 0.194302 0.197294 -0.643362
TREE: (human:0.072449,(mouse:0.026157,rat:0.028659):0.072449);
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