/usr/share/phast/data/exoniphy/mammals/hky.5'splice-5.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: 0.385999
BACKGROUND: 0.078768 0.054405 0.798693 0.068133
RATE_MAT:
-5.055733 0.043783 4.957120 0.054831
0.063389 -1.129014 0.642753 0.422872
0.488879 0.043783 -0.587492 0.054831
0.063389 0.337668 0.642753 -1.043809
TREE: (human:0.121346,(mouse:0.029477,rat:0.034283):0.121346);
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