/usr/share/phast/data/exoniphy/mammals/hky.cds3'ss.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: 0.253681 0.138866 0.494041 0.113412
RATE_MAT:
-1.512629 0.081055 1.365377 0.066198
0.148072 -0.749875 0.288367 0.313436
0.701097 0.081055 -0.848349 0.066198
0.148072 0.383782 0.288367 -0.820221
TREE: (human:0.035529,(mouse:0.015160,rat:0.015336):0.035529);
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