1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
|
# nucleic.pri
#
# Example of a prior file for DNA/RNA models.
# The values in this file are the HMMER 2 default settings.
Dirichlet # Strategy (mixture Dirichlet)
Nucleic # type of prior (Amino or Nucleic)
# Transitions
1 # Single component
1.0 # with probability = 1.0
0.7939 0.0278 0.0135 # m->m, m->i, m->d alpha's
0.1551 0.1331 # i->m, i->i alpha's
0.9002 0.5630 # d->m, d->d alpha's
# Match emissions
# The use of 1.0 for alpha's here makes a simple Laplace "plus-one" prior.
#
1 # single component
1.0 # with probability = 1.0
1.0 1.0 1.0 1.0
# Insert emissions
#
1 # Single component
1.0 # with probability 1.0
1.0 1.0 1.0 1.0
|
