Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

comparison orthologs/ucsb_hamster/lib/wisecfg/tm.pri @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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-1:000000000000 0:5b9a38ec4a39
1 #
2 #
3 # Ok - something hacked around for the Transmembrane model
4 #
5 # This is an example of a Brown-Haussler mixture Dirichlet prior.
6 #
7
8 Mix # Strategy (mixture Dirichlet)
9 Amino # type of prior (Amino or Nucleic)
10
11 # Transitions
12 2 # 2 component - first component an ungappy region.
13 0.3 # with probability = 1.0
14 10. 0.015 0.015 # m->m, m->i, m->d alpha's
15 10. 1.170 0.060 # i->m, i->i, i->d alpha's
16 10. 0.060 0.300 # d->m, d->i, d->d alpha's
17 0.7 # with probability = 1.0
18 2.970 0.015 0.015 # m->m, m->i, m->d alpha's
19 1.770 1.170 0.060 # i->m, i->i, i->d alpha's
20 2.640 0.060 0.300 # d->m, d->i, d->d alpha's
21
22 # A C D E F G H I K L M N P Q R S T V W Y
23
24 # ok
25 #
26 # 1st column meant to be a pretty heavy hyrdophobic prior thing.
27 #
28 # Match emissions
29 # A C D E F G H I K L M N P Q R S T V W Y
30 #
31 11 # 11 components
32 0.031
33 # A C D E F G H I K L M N P Q R S T V W Y
34 20. 15. 0.2 0.2 20. 4. 4. 20. 0.2 20. 20. 20. 4. 1. 0.2 4. 4. 20. 15. 15.
35 0.001
36 22.379 0.175 0.818 1.110 0.292 1.928 0.175 0.234 0.467 0.409 0.117 0.643 0.993 0.351 0.292 25.184 1.811 0.643 0.117 0.292
37 0.025
38 4.468 0.194 1.632 7.266 0.466 13.443 0.272 0.583 1.049 1.243 0.194 0.622 0.777 2.487 0.466 1.399 0.699 0.932 0.117 0.505
39 0.091
40 0.788 0.158 0.158 0.237 6.150 0.237 0.079 16.873 0.237 27.991 2.917 0.237 0.237 0.237 0.237 0.237 0.473 20.421 0.158 0.788
41 0.024
42 1.313 0.303 0.808 0.707 0.606 0.808 0.303 0.707 0.606 1.717 0.303 0.505 87.087 0.606 0.505 1.515 0.909 1.010 0.202 0.505
43 0.701
44 0.160 0.042 0.126 0.146 0.070 0.120 0.054 0.094 0.166 0.138 0.056 0.090 0.062 0.094 0.080 0.150 0.126 0.122 0.038 0.070
45 0.015
46 1.017 0.113 87.577 16.950 0.565 0.565 0.113 0.452 0.791 0.339 0.226 1.017 0.565 0.452 0.339 0.565 0.339 0.452 0.001 0.791
47 0.041
48 0.994 0.339 2.031 1.185 0.804 1.269 1.016 0.402 0.741 0.592 0.444 4.401 0.529 0.592 0.508 1.502 1.164 0.571 0.360 1.671
49 0.024
50 26.730 0.286 0.800 1.885 0.800 0.971 0.228 1.142 2.056 3.770 0.343 0.742 1.142 0.685 0.571 1.199 1.713 11.252 0.171 0.514
51 0.017
52 1.170 0.177 1.489 0.745 1.028 0.957 0.177 0.674 2.092 1.347 0.142 1.170 0.603 0.496 17.053 2.801 0.957 1.560 0.177 0.638
53 0.030
54 0.001 0.001 0.001 0.001 0.001 5793.873 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
55
56 ## Insert emissions
57 1 # Single component
58 1.0 # with probability 1.0
59 17430 6690 9370 9910 7950 17720 6720 7380 16100 17070 2950 8090 10140 7650 8180 13920 11710 12940 2100 5980
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