/usr/share/phast/data/exoniphy/mammals/hky.3'splice-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 11 12 | ALPHABET: A C G T
ORDER: 0
SUBST_MOD: HKY85
NRATECATS: 4
ALPHA: 3.186730
BACKGROUND: 0.243737 0.269043 0.207410 0.279810
RATE_MAT:
-0.924181 0.191276 0.533975 0.198930
0.173284 -1.041111 0.147457 0.720369
0.627500 0.191276 -1.017706 0.198930
0.173284 0.692649 0.147457 -1.013391
TREE: (human:0.209972,(mouse:0.072091,rat:0.073773):0.209972);
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