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

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #
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2 #
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 # Ok - something hacked around for the Transmembrane model
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 #
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 # This is an example of a Brown-Haussler mixture Dirichlet prior.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 #
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 Mix # Strategy (mixture Dirichlet)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 Amino # type of prior (Amino or Nucleic)
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10
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 # Transitions
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12 2 # 2 component - first component an ungappy region.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 0.3 # with probability = 1.0
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 10. 0.015 0.015 # m->m, m->i, m->d alpha's
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15 10. 1.170 0.060 # i->m, i->i, i->d alpha's
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16 10. 0.060 0.300 # d->m, d->i, d->d alpha's
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 0.7 # with probability = 1.0
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 2.970 0.015 0.015 # m->m, m->i, m->d alpha's
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19 1.770 1.170 0.060 # i->m, i->i, i->d alpha's
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 2.640 0.060 0.300 # d->m, d->i, d->d alpha's
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21
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 # A C D E F G H I K L M N P Q R S T V W Y
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23
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 # ok
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 #
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 # 1st column meant to be a pretty heavy hyrdophobic prior thing.
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27 #
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 # Match emissions
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29 # A C D E F G H I K L M N P Q R S T V W Y
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30 #
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 11 # 11 components
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32 0.031
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33 # A C D E F G H I K L M N P Q R S T V W Y
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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.
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35 0.001
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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
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37 0.025
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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
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39 0.091
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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
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41 0.024
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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
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43 0.701
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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
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45 0.015
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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
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47 0.041
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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
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49 0.024
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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
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51 0.017
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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
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53 0.030
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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
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55
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56 ## Insert emissions
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57 1 # Single component
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58 1.0 # with probability 1.0
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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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