/usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-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 | ALPHABET: A C G T
ORDER: 0
SUBST_MOD: HKY85
BACKGROUND: 0.103012 0.029101 0.796692 0.071196
RATE_MAT:
-3.674777 0.040886 3.533863 0.100029
0.144729 -1.579862 1.119331 0.315802
0.456926 0.040886 -0.597840 0.100029
0.144729 0.129082 1.119331 -1.393141
TREE: (human:0.023490,(mouse:0.010685,rat:0.012583):0.023490);
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