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diff 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/ucsb_hamster/lib/wisecfg/tm.pri	Tue Mar 11 12:19:13 2014 -0700
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+#
+#
+# Ok - something hacked around for the Transmembrane model
+#
+# This is an example of a Brown-Haussler mixture Dirichlet prior.
+#
+
+Mix   # Strategy (mixture Dirichlet)
+Amino # type of prior (Amino or Nucleic)
+
+# Transitions
+2                   # 2 component - first component an ungappy region.
+0.3                 #   with probability = 1.0
+10.    0.015 0.015   # m->m, m->i, m->d alpha's
+10.    1.170 0.060   # i->m, i->i, i->d alpha's
+10.    0.060 0.300   # d->m, d->i, d->d alpha's
+0.7                 #   with probability = 1.0
+2.970 0.015 0.015   # m->m, m->i, m->d alpha's
+1.770 1.170 0.060   # i->m, i->i, i->d alpha's
+2.640 0.060 0.300   # d->m, d->i, d->d alpha's
+
+# A C   D   E   F G H I   K   L  M  N P Q R S  T  V  W  Y 
+
+# ok 
+#
+# 1st column meant to be a pretty heavy hyrdophobic prior thing.
+#
+# Match emissions
+# A C D E F G H I K L M N P Q R S T V W Y 
+#
+11	# 11 components
+0.031
+# A     C     D     E     F    G     H      I      K    L      M    N     P    Q      R    S      T     V     W    Y 
+20.    15.   0.2   0.2   20.   4.    4.    20.    0.2   20.   20.   20.   4.   1.    0.2   4.     4.   20.   15.   15.
+0.001
+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 
+0.025 
+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 
+0.091 
+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 
+0.024 
+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 
+0.701 
+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 
+0.015 
+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 
+0.041 
+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 
+0.024 
+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 
+0.017 
+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 
+0.030 
+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 
+
+## Insert emissions
+1                   # Single component
+1.0                 #    with probability 1.0
+17430 6690 9370 9910 7950 17720 6720 7380 16100 17070 2950 8090 10140 7650 8180 13920 11710 12940 2100 5980
+
+
+
+