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:
- Compute the MLEs for each of the 203 models, starting with the most general (REV).
- 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.
- If all 202 models have been rejected, then REV is the model of choice, otherwise
proceed to step 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.
- If all but one model have been rejected, report the remaining model,
otherwise go to step 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.
|