/usr/share/phast/data/phastCons/simple-coding.hmm 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 13 14 15 16 17 18 19 | TRANSITION_MATRIX:
A B C D E
9.998439e-01 1.054441e-04 2.610457e-05 1.430363e-05 1.022429e-05
5.841376e-03 9.941586e-01 5.944372e-08 0.000000e+00 0.000000e+00
6.792362e-03 1.507471e-07 3.014941e-07 9.932072e-01 0.000000e+00
4.831518e-03 1.508624e-07 0.000000e+00 0.000000e+00 9.951683e-01
9.731452e-03 4.528223e-07 9.902679e-01 1.509408e-07 0.000000e+00
EQUILIBRIUM_FREQUENCIES:
9.754531e-01
1.760826e-02
2.314474e-03
2.312705e-03
2.311504e-03
BEGIN_TRANSITIONS:
1.000000e+00
0.000000e+00
0.000000e+00
0.000000e+00
0.000000e+00
|