/usr/share/phast/data/exoniphy/mammals/hky.prestart-4.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: 0.959598
BACKGROUND: 0.158202 0.483626 0.283618 0.074554
RATE_MAT:
-1.551398 0.317458 1.185002 0.048938
0.103846 -0.601515 0.186170 0.311498
0.660995 0.317458 -1.027392 0.048938
0.103846 2.020666 0.186170 -2.310683
TREE: (human:0.130182,(mouse:0.035219,rat:0.045576):0.130182);
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