/usr/share/phast/data/exoniphy/mammals/hky.3'splice-4.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 11 12 | ALPHABET: A C G T
ORDER: 0
SUBST_MOD: HKY85
NRATECATS: 4
ALPHA: 2.308594
BACKGROUND: 0.053016 0.648785 0.001767 0.296431
RATE_MAT:
-0.630415 0.429773 0.004278 0.196364
0.035119 -0.753740 0.001171 0.717450
0.128315 0.429773 -0.754452 0.196364
0.035119 1.570251 0.001171 -1.606541
TREE: (human:0.134188,(mouse:0.041703,rat:0.047448):0.134188);
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