/usr/share/phast/data/exoniphy/mammals/hky.prestart-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 11 12 | ALPHABET: A C G T
ORDER: 0
SUBST_MOD: HKY85
NRATECATS: 4
ALPHA: 0.689710
BACKGROUND: 0.287138 0.403495 0.178944 0.130423
RATE_MAT:
-0.940353 0.305566 0.536017 0.098769
0.217449 -0.743639 0.135514 0.390676
0.860107 0.305566 -1.264443 0.098769
0.217449 1.208650 0.135514 -1.561613
TREE: (human:0.118331,(mouse:0.036261,rat:0.036762):0.118331);
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