/usr/share/phast/data/exoniphy/mammals/hky.prestart-1.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: 1.730956
BACKGROUND: 0.234295 0.398829 0.248177 0.118699
RATE_MAT:
-1.118303 0.331049 0.688728 0.098526
0.194477 -0.729883 0.206000 0.329406
0.650202 0.331049 -1.079777 0.098526
0.194477 1.106807 0.206000 -1.507284
TREE: (human:0.120499,(mouse:0.037528,rat:0.039043):0.120499);
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