/usr/share/phast/data/exoniphy/mammals/hky.3'splice-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: 0.883721
BACKGROUND: 0.081422 0.347023 0.062209 0.509346
RATE_MAT:
-0.861312 0.294159 0.135399 0.431754
0.069019 -1.230357 0.052732 1.108606
0.177218 0.294159 -0.903131 0.431754
0.069019 0.755306 0.052732 -0.877057
TREE: (human:0.174641,(mouse:0.052659,rat:0.057246):0.174641);
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