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  HyPhy Documentation: Standard Analyses: CodonModelCompare.bf

     Summary: Given a codon data file, and a tree and a model class, CodonModelCompare attempts to find which model from the class provides the best fit for the data. The overall class for the models in the class of general time reversible models nucleotide models mated with the MG94 model which compensates for synonymous/non-synonymous bias. The equilibrium frequencies used are the 9 parameter observed frequencies model, i.e.

     There are 203 models in this class. Each can be specified by a 6 number code, e.g. 010010 for HKY85, which determines the six above-diagonal rates (the matrix is symmetric in rates). A different number in the designation indicates that a separate rate parameters should be used for that rate (010010 will thus have two rate parameters), and all the matrix entries with the same number designation will share the same rate - 010010 means:

     The procedure for model testing is as follows:

  1. Compute the MLEs for each of the 203 models, starting with the most general (REV).
  2. For each of the 202 models which are particular cases of REV, compute the likelihood ratio test using the model as null and REV as alternative, and reject the model if the p-value is below a user-specified threshold.
  3. If all 202 models have been rejected, then REV is the model of choice, otherwise proceed to step 4.
  4. For all remaining models: look for a pair of nested models, perform the LRT using the more general as an alternative; reject null if the p-value is below a user-specified threshold, reject the alternative otherwise.
  5. If all but one model have been rejected, report the remaining model, otherwise go to step 6.
  6. Rank the remaining models using AIC (Akaike Information Criterion) =
    2(-log likelihood+number of parameters). Report the model with the lowest AIC.
Note that since multiple tests are performed, the rejection level is NOT the p-value for the final model; Bonferroni correction should be applied; however the number of tests in step 4 can't be determined a-priori.

     Input: A codon data file in any recognizable format. Any of the predefined genetic code translation tables can be used to interpret the data.
    A starting tree is also needed. It may either be present in the data file, or reside in a separate (Newick string) file.
    The user will be prompted to choose whether the models tested should be:

  • Global: rate parameters shared by all branches, branch lengths are idependent
  • Rate Variation(+HM): rate parameters shared by all branches, branch lengths are idependent, rate variation multiplier tacked on to each rate matrix entry.

    The user will also specify model rejection level.

    Models: Selected by the analysis

    Output: CodonModelCompare prints out the results in a table for steps 1 and 2; if step 4 is performed - the result of each nested test is printed; if step 6 is performed - the summary table of remaining models is printed; finally, the best model is reported. For example look:

Model rejection level (e.g. 0.05):0.05

(012345) Full Model ln-lik =  -823.929. Parameter Count=9


#   |  Model   | # prm |    lnL    |      LRT       |    AIC     |   P-Value        |
----|----------|-------|-----------|----------------|------------|------------------|
1   | (000000) |     4 |  -852.395 |         56.932 |  1712.79   |  5.22319e-11     |(*)
2   | (000001) |     5 |  -848.986 |         50.114 |  1707.97   |  3.41848e-10     |(*)
3   | (000010) |     5 |  -849.284 |         50.711 |  1708.57   |  2.5651e-10      |(*)
4   | (000011) |     5 |  -852.062 |         56.267 |  1714.12   |  1.76241e-11     |(*)
5   | (000012) |     6 |  -846.835 |         45.812 |  1705.67   |  6.21743e-10     |(*)
6   | (000100) |     5 |  -850.937 |         54.017 |  1711.87   |  5.21997e-11     |(*)
7   | (000101) |     5 |  -847.243 |         46.629 |  1704.49   |  1.82165e-09     |(*)
8   | (000102) |     6 |  -847.167 |         46.476 |  1706.33   |  4.49214e-10     |(*)
9   | (000110) |     5 |  -851.312 |         54.766 |  1712.62   |  3.63736e-11     |(*)
10  | (000111) |     5 |  -852.394 |         56.930 |  1714.79   |  1.27958e-11     |(*)
11  | (000112) |     6 |  -848.499 |         49.141 |  1709      |  1.21716e-10     |(*)
12  | (000120) |     6 |  -848.137 |         48.417 |  1708.27   |  1.73593e-10     |(*)
13  | (000121) |     6 |  -845.578 |         43.299 |  1703.16   |  2.12626e-09     |(*)
14  | (000122) |     6 |  -850.762 |         53.667 |  1713.52   |  1.32164e-11     |(*)
15  | (000123) |     7 |  -845.545 |         43.232 |  1705.09   |  4.09497e-10     |(*)
16  | (001000) |     5 |  -837.055 |         26.253 |  1684.11   |  2.81336e-05     |(*)
17  | (001001) |     5 |  -831.399 |         14.940 |  1672.8    |  0.00482836      |(*)
18  | (001002) |     6 |  -831.391 |         14.924 |  1674.78   |  0.00188272      |(*)
19  | (001010) |     5 |  -848.787 |         49.717 |  1707.57   |  4.13725e-10     |(*)
20  | (001011) |     5 |  -844.342 |         40.827 |  1698.68   |  2.91891e-08     |(*)
21  | (001012) |     6 |  -842.846 |         37.835 |  1697.69   |  3.06318e-08     |(*)
22  | (001020) |     6 |  -836.79  |         25.723 |  1685.58   |  1.08986e-05     |(*)
23  | (001021) |     6 |  -831.37  |         14.883 |  1674.74   |  0.00191945      |(*)
24  | (001022) |     6 |  -836.04  |         24.222 |  1684.08   |  2.24465e-05     |(*)
25  | (001023) |     7 |  -831.363 |         14.868 |  1676.73   |  0.000590858     |(*)
26  | (001100) |     5 |  -834.007 |         20.157 |  1678.01   |  0.000465095     |(*)
27  | (001101) |     5 |  -827.71  |          7.563 |  1665.42   |  0.10895         |
28  | (001102) |     6 |  -827.594 |          7.331 |  1667.19   |  0.0620728       |
29  | (001110) |     5 |  -846.963 |         46.069 |  1703.93   |  2.38303e-09     |(*)
30  | (001111) |     5 |  -840.992 |         34.127 |  1691.98   |  7.01811e-07     |(*)
31  | (001112) |     6 |  -839.504 |         31.150 |  1691.01   |  7.9028e-07      |(*)
32  | (001120) |     6 |  -833.893 |         19.929 |  1679.79   |  0.000175609     |(*)
33  | (001121) |     6 |  -827.654 |          7.450 |  1667.31   |  0.0588647       |
34  | (001122) |     6 |  -832.117 |         16.377 |  1676.23   |  0.000948817     |(*)
35  | (001123) |     7 |  -827.541 |          7.224 |  1669.08   |  0.0269953       |(*)
36  | (001200) |     6 |  -833.995 |         20.133 |  1679.99   |  0.000159311     |(*)
37  | (001201) |     6 |  -827.709 |          7.561 |  1667.42   |  0.0560096       |
38  | (001202) |     6 |  -827.64  |          7.423 |  1667.28   |  0.0595604       |
39  | (001203) |     7 |  -827.594 |          7.330 |  1669.19   |  0.0255983       |(*)
40  | (001210) |     6 |  -846.462 |         45.067 |  1704.92   |  8.95507e-10     |(*)
41  | (001211) |     6 |  -840.419 |         32.981 |  1692.84   |  3.25053e-07     |(*)
42  | (001212) |     6 |  -838.7   |         29.543 |  1689.4    |  1.72227e-06     |(*)
43  | (001213) |     7 |  -838.678 |         29.497 |  1691.36   |  3.93279e-07     |(*)
44  | (001220) |     6 |  -836.937 |         26.015 |  1685.87   |  9.46655e-06     |(*)
45  | (001221) |     6 |  -830.75  |         13.643 |  1673.5    |  0.00343436      |(*)
46  | (001222) |     6 |  -834.012 |         20.166 |  1680.02   |  0.000156804     |(*)
47  | (001223) |     7 |  -830.728 |         13.599 |  1675.46   |  0.00111415      |(*)
48  | (001230) |     7 |  -833.883 |         19.908 |  1681.77   |  4.75429e-05     |(*)
49  | (001231) |     7 |  -827.651 |          7.444 |  1669.3    |  0.0241857       |(*)
50  | (001232) |     7 |  -827.592 |          7.326 |  1669.18   |  0.0256575       |(*)
51  | (001233) |     7 |  -832.115 |         16.373 |  1678.23   |  0.000278332     |(*)
52  | (001234) |     8 |  -827.541 |          7.224 |  1671.08   |  0.0071954       |(*)
53  | (010000) |     5 |  -838.242 |         28.626 |  1686.48   |  9.30977e-06     |(*)
54  | (010001) |     5 |  -846.818 |         45.778 |  1703.64   |  2.73871e-09     |(*)
55  | (010002) |     6 |  -835.181 |         22.505 |  1682.36   |  5.12136e-05     |(*)
56  | (010010) |     5 |  -829.901 |         11.945 |  1669.8    |  0.0177645       |(*)
57  | (010011) |     5 |  -838.205 |         28.552 |  1686.41   |  9.63993e-06     |(*)
58  | (010012) |     6 |  -829.17  |         10.482 |  1670.34   |  0.0148839       |(*)
59  | (010020) |     6 |  -828.79  |          9.722 |  1669.58   |  0.0210876       |(*)
60  | (010021) |     6 |  -838.201 |         28.544 |  1688.4    |  2.79199e-06     |(*)
61  | (010022) |     6 |  -833.633 |         19.409 |  1679.27   |  0.000225006     |(*)
62  | (010023) |     7 |  -827.895 |          7.931 |  1669.79   |  0.0189541       |(*)
63  | (010100) |     5 |  -842.752 |         37.647 |  1695.5    |  1.32499e-07     |(*)
64  | (010101) |     5 |  -848.846 |         49.834 |  1707.69   |  3.91019e-10     |(*)
65  | (010102) |     6 |  -840.242 |         32.626 |  1692.48   |  3.86172e-07     |(*)
66  | (010110) |     5 |  -833.426 |         18.994 |  1676.85   |  0.00078823      |(*)
67  | (010111) |     5 |  -840.933 |         34.009 |  1691.87   |  7.4201e-07      |(*)
68  | (010112) |     6 |  -832.433 |         17.009 |  1676.87   |  0.000703868     |(*)
69  | (010120) |     6 |  -832.832 |         17.806 |  1677.66   |  0.000482395     |(*)
70  | (010121) |     6 |  -840.88  |         33.902 |  1693.76   |  2.07777e-07     |(*)
71  | (010122) |     6 |  -837.574 |         27.290 |  1687.15   |  5.11769e-06     |(*)
72  | (010123) |     7 |  -831.86  |         15.863 |  1677.72   |  0.000359227     |(*)
73  | (010200) |     6 |  -837.949 |         28.040 |  1687.9    |  3.56231e-06     |(*)
74  | (010201) |     6 |  -846.29  |         44.723 |  1704.58   |  1.05969e-09     |(*)
75  | (010202) |     6 |  -835.172 |         22.487 |  1682.34   |  5.16455e-05     |(*)
76  | (010203) |     7 |  -834.634 |         21.410 |  1683.27   |  2.24368e-05     |(*)
77  | (010210) |     6 |  -829.88  |         11.903 |  1671.76   |  0.00772135      |(*)
78  | (010211) |     6 |  -838.118 |         28.379 |  1688.24   |  3.02355e-06     |(*)
79  | (010212) |     6 |  -829.313 |         10.769 |  1670.63   |  0.0130449       |(*)
80  | (010213) |     7 |  -829.138 |         10.418 |  1672.28   |  0.00546743      |(*)
81  | (010220) |     6 |  -830.198 |         12.538 |  1672.4    |  0.00574953      |(*)
82  | (010221) |     6 |  -840.486 |         33.115 |  1692.97   |  3.0462e-07      |(*)
83  | (010222) |     6 |  -834.225 |         20.592 |  1680.45   |  0.000127976     |(*)
84  | (010223) |     7 |  -829.24  |         10.622 |  1672.48   |  0.00493742      |(*)
85  | (010230) |     7 |  -828.79  |          9.723 |  1671.58   |  0.00774061      |(*)
86  | (010231) |     7 |  -838.11  |         28.361 |  1690.22   |  6.94045e-07     |(*)
87  | (010232) |     7 |  -828.205 |          8.553 |  1670.41   |  0.0138923       |(*)
88  | (010233) |     7 |  -833.634 |         19.411 |  1681.27   |  6.09545e-05     |(*)
89  | (010234) |     8 |  -827.885 |          7.912 |  1671.77   |  0.00491016      |(*)
90  | (011000) |     5 |  -852.393 |         56.929 |  1714.79   |  1.28006e-11     |(*)
91  | (011001) |     5 |  -851.576 |         55.295 |  1713.15   |  2.81836e-11     |(*)
92  | (011002) |     6 |  -848.879 |         49.900 |  1709.76   |  8.39091e-11     |(*)
93  | (011010) |     5 |  -849.67  |         51.482 |  1709.34   |  1.77033e-10     |(*)
94  | (011011) |     5 |  -852.021 |         56.185 |  1714.04   |  1.83424e-11     |(*)
95  | (011012) |     6 |  -847.746 |         47.635 |  1707.49   |  2.54704e-10     |(*)
96  | (011020) |     6 |  -847.674 |         47.490 |  1707.35   |  2.73421e-10     |(*)
97  | (011021) |     6 |  -849.161 |         50.464 |  1710.32   |  6.36238e-11     |(*)
98  | (011022) |     6 |  -851.833 |         55.809 |  1715.67   |  4.61498e-12     |(*)
99  | (011023) |     7 |  -846.244 |         44.630 |  1706.49   |  2.03591e-10     |(*)
100 | (011100) |     5 |  -852.132 |         56.406 |  1714.26   |  1.64788e-11     |(*)
101 | (011101) |     5 |  -850.398 |         52.938 |  1710.8    |  8.77994e-11     |(*)
102 | (011102) |     6 |  -848.141 |         48.425 |  1708.28   |  1.72896e-10     |(*)
103 | (011110) |     5 |  -851.151 |         54.444 |  1712.3    |  4.24888e-11     |(*)
104 | (011111) |     5 |  -852.401 |         56.944 |  1714.8    |  1.27098e-11     |(*)
105 | (011112) |     6 |  -848.824 |         49.790 |  1709.65   |  8.85789e-11     |(*)
106 | (011120) |     6 |  -848.689 |         49.520 |  1709.38   |  1.01103e-10     |(*)
107 | (011121) |     6 |  -849.234 |         50.611 |  1710.47   |  5.92116e-11     |(*)
108 | (011122) |     6 |  -852.05  |         56.242 |  1716.1    |  3.73068e-12     |(*)
109 | (011123) |     7 |  -846.818 |         45.778 |  1707.64   |  1.14655e-10     |(*)
110 | (011200) |     6 |  -850.856 |         53.854 |  1713.71   |  1.20539e-11     |(*)
111 | (011201) |     6 |  -849.389 |         50.921 |  1710.78   |  5.08502e-11     |(*)
112 | (011202) |     6 |  -846.795 |         45.733 |  1705.59   |  6.46462e-10     |(*)
113 | (011203) |     7 |  -846.765 |         45.673 |  1707.53   |  1.20857e-10     |(*)
114 | (011210) |     6 |  -849.246 |         50.635 |  1710.49   |  5.85244e-11     |(*)
115 | (011211) |     6 |  -850.93  |         54.002 |  1713.86   |  1.12107e-11     |(*)
116 | (011212) |     6 |  -846.994 |         46.131 |  1705.99   |  5.31951e-10     |(*)
117 | (011213) |     7 |  -846.859 |         45.861 |  1707.72   |  1.10015e-10     |(*)
118 | (011220) |     6 |  -850.57  |         53.282 |  1713.14   |  1.5962e-11      |(*)
119 | (011221) |     6 |  -851.273 |         54.688 |  1714.55   |  8.00138e-12     |(*)
120 | (011222) |     6 |  -852.398 |         56.939 |  1716.8    |  2.64844e-12     |(*)
121 | (011223) |     7 |  -848.447 |         49.037 |  1710.89   |  2.24806e-11     |(*)
122 | (011230) |     7 |  -847.25  |         46.642 |  1708.5    |  7.44427e-11     |(*)
123 | (011231) |     7 |  -848.133 |         48.409 |  1710.27   |  3.0776e-11      |(*)
124 | (011232) |     7 |  -845.502 |         43.146 |  1705      |  4.27451e-10     |(*)
125 | (011233) |     7 |  -850.766 |         53.673 |  1715.53   |  2.2129e-12      |(*)
126 | (011234) |     8 |  -845.451 |         43.044 |  1706.9    |  5.35316e-11     |(*)
127 | (012000) |     6 |  -829.209 |         10.561 |  1670.42   |  0.0143511       |(*)
128 | (012001) |     6 |  -835.688 |         23.519 |  1683.38   |  3.14806e-05     |(*)
129 | (012002) |     6 |  -826.635 |          5.413 |  1665.27   |  0.143926        |
130 | (012003) |     7 |  -826.635 |          5.412 |  1667.27   |  0.0668125       |
131 | (012010) |     6 |  -827.708 |          7.559 |  1667.42   |  0.0560606       |
132 | (012011) |     6 |  -834.084 |         20.310 |  1680.17   |  0.000146362     |(*)
133 | (012012) |     6 |  -826.273 |          4.689 |  1664.55   |  0.19603         |
134 | (012013) |     7 |  -826.271 |          4.684 |  1666.54   |  0.0961187       |
135 | (012020) |     6 |  -838.221 |         28.585 |  1688.44   |  2.7379e-06      |(*)
136 | (012021) |     6 |  -846.574 |         45.290 |  1705.15   |  8.02827e-10     |(*)
137 | (012022) |     6 |  -837.69  |         27.522 |  1687.38   |  4.57486e-06     |(*)
138 | (012023) |     7 |  -835.114 |         22.370 |  1684.23   |  1.38798e-05     |(*)
139 | (012030) |     7 |  -826.221 |          4.584 |  1666.44   |  0.101066        |
140 | (012031) |     7 |  -834.013 |         20.169 |  1682.03   |  4.17198e-05     |(*)
141 | (012032) |     7 |  -824.903 |          1.949 |  1663.81   |  0.377337        |
142 | (012033) |     7 |  -828.768 |          9.679 |  1671.54   |  0.00791295      |(*)
143 | (012034) |     8 |  -824.899 |          1.941 |  1665.8    |  0.163559        |
144 | (012100) |     6 |  -833.446 |         19.034 |  1678.89   |  0.000268987     |(*)
145 | (012101) |     6 |  -836.941 |         26.024 |  1685.88   |  9.42662e-06     |(*)
146 | (012102) |     6 |  -830.132 |         12.407 |  1672.26   |  0.00611087      |(*)
147 | (012103) |     7 |  -830.131 |         12.405 |  1674.26   |  0.00202441      |(*)
148 | (012110) |     6 |  -831.347 |         14.836 |  1674.69   |  0.00196194      |(*)
149 | (012111) |     6 |  -836.184 |         24.511 |  1684.37   |  1.95345e-05     |(*)
150 | (012112) |     6 |  -829.351 |         10.845 |  1670.7    |  0.0125949       |(*)
151 | (012113) |     7 |  -829.327 |         10.796 |  1672.65   |  0.00452468      |(*)
152 | (012120) |     6 |  -842.749 |         37.641 |  1697.5    |  3.367e-08       |(*)
153 | (012121) |     6 |  -848.233 |         48.609 |  1708.47   |  1.58001e-10     |(*)
154 | (012122) |     6 |  -842.049 |         36.240 |  1696.1    |  6.66363e-08     |(*)
155 | (012123) |     7 |  -840.075 |         32.293 |  1694.15   |  9.71819e-08     |(*)
156 | (012130) |     7 |  -830.793 |         13.728 |  1675.59   |  0.00104464      |(*)
157 | (012131) |     7 |  -836.169 |         24.481 |  1686.34   |  4.83011e-06     |(*)
158 | (012132) |     7 |  -829.022 |         10.187 |  1672.04   |  0.00613577      |(*)
159 | (012133) |     7 |  -833.302 |         18.746 |  1680.6    |  8.50003e-05     |(*)
160 | (012134) |     8 |  -828.995 |         10.133 |  1673.99   |  0.00145641      |(*)
161 | (012200) |     6 |  -827.88  |          7.903 |  1667.76   |  0.0480632       |(*)
162 | (012201) |     6 |  -833.534 |         19.211 |  1679.07   |  0.000247214     |(*)
163 | (012202) |     6 |  -824.624 |          1.390 |  1661.25   |  0.707852        |
164 | (012203) |     7 |  -824.602 |          1.347 |  1663.2    |  0.510016        |
165 | (012210) |     6 |  -827.102 |          6.346 |  1666.2    |  0.0959448       |
166 | (012211) |     6 |  -832.77  |         17.683 |  1677.54   |  0.000511209     |(*)
167 | (012212) |     6 |  -825.189 |          2.521 |  1662.38   |  0.471431        |
168 | (012213) |     7 |  -825.167 |          2.477 |  1664.33   |  0.289754        |
169 | (012220) |     6 |  -838.239 |         28.620 |  1688.48   |  2.69085e-06     |(*)
170 | (012221) |     6 |  -845.999 |         44.140 |  1704      |  1.40952e-09     |(*)
171 | (012222) |     6 |  -837.02  |         26.183 |  1686.04   |  8.73026e-06     |(*)
172 | (012223) |     7 |  -834.733 |         21.608 |  1683.47   |  2.03147e-05     |(*)
173 | (012230) |     7 |  -825.757 |          3.656 |  1665.51   |  0.160758        |
174 | (012231) |     7 |  -832.75  |         17.642 |  1679.5    |  0.000147612     |(*)
175 | (012232) |     7 |  -823.939 |          0.020 |  1661.88   |  0.990286        |
176 | (012233) |     7 |  -827.848 |          7.839 |  1669.7    |  0.0198482       |(*)
177 | (012234) |     8 |  -823.931 |          0.004 |  1663.86   |  0.949749        |
178 | (012300) |     7 |  -827.849 |          7.841 |  1669.7    |  0.0198313       |(*)
179 | (012301) |     7 |  -833.513 |         19.168 |  1681.03   |  6.88075e-05     |(*)
180 | (012302) |     7 |  -824.622 |          1.386 |  1663.24   |  0.500133        |
181 | (012303) |     7 |  -824.617 |          1.377 |  1663.23   |  0.502296        |
182 | (012304) |     8 |  -824.601 |          1.344 |  1665.2    |  0.246315        |
183 | (012310) |     7 |  -827.09  |          6.322 |  1668.18   |  0.0423792       |(*)
184 | (012311) |     7 |  -832.752 |         17.647 |  1679.5    |  0.000147214     |(*)
185 | (012312) |     7 |  -825.188 |          2.518 |  1664.38   |  0.283961        |
186 | (012313) |     7 |  -825.171 |          2.485 |  1664.34   |  0.288713        |
187 | (012314) |     8 |  -825.164 |          2.471 |  1666.33   |  0.115987        |
188 | (012320) |     7 |  -837.945 |         28.033 |  1689.89   |  8.18011e-07     |(*)
189 | (012321) |     7 |  -845.584 |         43.311 |  1705.17   |  3.936e-10       |(*)
190 | (012322) |     7 |  -836.664 |         25.471 |  1687.33   |  2.94468e-06     |(*)
191 | (012323) |     7 |  -834.506 |         21.155 |  1683.01   |  2.548e-05       |(*)
192 | (012324) |     8 |  -834.16  |         20.463 |  1684.32   |  6.0798e-06      |(*)
193 | (012330) |     7 |  -827.743 |          7.628 |  1669.49   |  0.0220642       |(*)
194 | (012331) |     7 |  -835.423 |         22.989 |  1684.85   |  1.01873e-05     |(*)
195 | (012332) |     7 |  -826.218 |          4.578 |  1666.44   |  0.101356        |
196 | (012333) |     7 |  -829.19  |         10.523 |  1672.38   |  0.00518704      |(*)
197 | (012334) |     8 |  -826.21  |          4.563 |  1668.42   |  0.0326614       |(*)
198 | (012340) |     8 |  -825.722 |          3.587 |  1667.44   |  0.0582289       |
199 | (012341) |     8 |  -832.726 |         17.594 |  1681.45   |  2.73384e-05     |(*)
200 | (012342) |     8 |  -823.937 |          0.017 |  1663.87   |  0.896887        |
201 | (012343) |     8 |  -823.931 |          0.004 |  1663.86   |  0.951762        |
202 | (012344) |     8 |  -827.806 |          7.754 |  1671.61   |  0.00535928      |(*)

--------------------------
   (*) => p-Value < 0.05
Rejected 171 models.

Performing nested tests on the remaining models...
H: (001101) A: (001102).  P-Value=     0.630. Failed to reject H. Discarding A.
H: (001101) A: (001121).  P-Value=     0.736. Failed to reject H. Discarding A.
H: (001101) A: (001201).  P-Value=     0.962. Failed to reject H. Discarding A.
H: (001101) A: (001202).  P-Value=     0.708. Failed to reject H. Discarding A.
H: (001101) A: (012202).  P-Value=     0.013. Rejected H.
H: (012002) A: (012003).  P-Value=     0.970. Failed to reject H. Discarding A.
H: (012002) A: (012032).  P-Value=     0.063. Failed to reject H. Discarding A.
H: (012002) A: (012034).  P-Value=     0.176. Failed to reject H. Discarding A.
H: (012002) A: (012302).  P-Value=     0.045. Rejected H.
H: (012010) A: (012013).  P-Value=     0.090. Failed to reject H. Discarding A.
H: (012010) A: (012030).  P-Value=     0.085. Failed to reject H. Discarding A.
H: (012010) A: (012313).  P-Value=     0.024. Rejected H.
H: (012012) A: (012312).  P-Value=     0.141. Failed to reject H. Discarding A.
H: (012012) A: (012314).  P-Value=     0.330. Failed to reject H. Discarding A.
H: (012012) A: (012342).  P-Value=     0.097. Failed to reject H. Discarding A.
H: (012202) A: (012203).  P-Value=     0.835. Failed to reject H. Discarding A.
H: (012202) A: (012232).  P-Value=     0.242. Failed to reject H. Discarding A.
H: (012202) A: (012234).  P-Value=     0.500. Failed to reject H. Discarding A.
H: (012202) A: (012302).  P-Value=     0.947. Failed to reject H. Discarding A.
H: (012202) A: (012303).  P-Value=     0.909. Failed to reject H. Discarding A.
H: (012202) A: (012304).  P-Value=     0.977. Failed to reject H. Discarding A.
H: (012202) A: (012343).  P-Value=     0.500. Failed to reject H. Discarding A.
H: (012210) A: (012213).  P-Value=     0.049. Rejected H.
H: (012212) A: (012213).  P-Value=     0.834. Failed to reject H. Discarding A.
H: (012212) A: (012313).  P-Value=     0.848. Failed to reject H. Discarding A.
H: (012230) A: (012340).  P-Value=     0.793. Failed to reject H. Discarding A.


Remaining models:

#   |  Model   | # prm |    lnL    |      LRT       |    AIC     |   P-Value        |
----|----------|-------|-----------|----------------|------------|------------------|
133 | (012012) |     6 |  -826.273 |          4.689 |  1664.55   |  0.19603         |
163 | (012202) |     6 |  -824.624 |          1.390 |  1661.25   |  0.707852        |
167 | (012212) |     6 |  -825.189 |          2.521 |  1662.38   |  0.471431        |
173 | (012230) |     7 |  -825.757 |          3.656 |  1665.51   |  0.160758        |
195 | (012332) |     7 |  -826.218 |          4.578 |  1666.44   |  0.101356        |

AIC based winner: (012202) with AIC = 1661.25

+---+-----+-----+-----+-----+
|   |  A  |  C  |  G  |  T  |
+---+-----+-----+-----+-----+
| A |  *  |  a  |  b  |  c  |
+---+-----+-----+-----+-----+
| C |  a  |  *  |  c  |  a  |
+---+-----+-----+-----+-----+
| G |  b  |  c  |  *  |  c  |
+---+-----+-----+-----+-----+
| T |  c  |  a  |  c  |  *  |
+---+-----+-----+-----+-----+

     Result Processing Tools: None applicable.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002