/usr/share/phast/data/exoniphy/mammals/hky.3'splice-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 11 12 | ALPHABET: A C G T
ORDER: 0
SUBST_MOD: HKY85
NRATECATS: 4
ALPHA: 1.127238
BACKGROUND: 0.082850 0.297987 0.060245 0.558918
RATE_MAT:
-0.833133 0.240755 0.140805 0.451572
0.066938 -1.421930 0.048674 1.306318
0.193640 0.240755 -0.885967 0.451572
0.066938 0.696463 0.048674 -0.812075
TREE: (human:0.178564,(mouse:0.052540,rat:0.060485):0.178564);
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