TIM2 model

[sereina]

hi all,

has anyone used before the substitution model TIM2? i´m not 100% sure that i implemented it correctly and was wondering if soembody could please confirm it? and is there a list of more substitution models than the ones from the wiki page available?

many thanks in advance, sereina

[C.-j. Mei]

There are 80+ models. Here is a list of them (from model test). We have a application to modeltest a set of sequence; select the best fitting model and create the corresponding XML input automatically.

 

CJ from ASU

 

Model             -lnL    K         AIC      delta      weight cumWeight
------------------------------------------------------------------------
TIM1+I+G     3970.5425   196   8333.0850     0.0000      0.3306    0.3306
TIM1+G       3972.4207   195   8334.8415     1.7565      0.1374    0.4679
GTR+I+G      3970.0795   198   8336.1590     3.0740      0.0711    0.5390
TIM1+I       3973.1116   195   8336.2232     3.1382      0.0688    0.6079
TPM1uf+I+G   3973.1877   195   8336.3754     3.2904      0.0638    0.6717
TIM1ef+I+G   3975.2895   193   8336.5789     3.4939      0.0576    0.7293
TPM1uf+G     3974.8314   194   8337.6628     4.5778      0.0335    0.7628
GTR+G        3971.9925   197   8337.9850     4.9000      0.0285    0.7913
TIM1ef+G     3977.1346   192   8338.2693     5.1843      0.0247    0.8161
TPM1uf+I     3975.1993   194   8338.3986     5.3136      0.0232    0.8393
TPM1+I+G     3977.3284   192   8338.6568     5.5718      0.0204    0.8597
SYM+I+G      3974.5927   195   8339.1854     6.1004      0.0157    0.8753
TIM1ef+I     3977.6854   192   8339.3709     6.2859      0.0143    0.8896
GTR+I        3972.6886   197   8339.3773     6.2923      0.0142    0.9038
TVM+I+G      3972.7290   197   8339.4580     6.3730      0.0137    0.9174
TPM1+G       3978.9981   191   8339.9961     6.9111      0.0104    0.9279
TPM1+I       3979.3198   191   8340.6396     7.5546      0.0076    0.9354
TVM+G        3974.4049   196   8340.8098     7.7248      0.0069    0.9424
SYM+G        3976.4704   194   8340.9407     7.8557      0.0065    0.9489
TIM2+I+G     3974.5284   196   8341.0568     7.9718      0.0061    0.9550
TIM3+I+G     3974.6190   196   8341.2380     8.1530      0.0056    0.9607
TVMef+I+G    3976.6226   194   8341.2452     8.1602      0.0056    0.9662
TVM+I        3974.8167   196   8341.6335     8.5485      0.0046    0.9708
SYM+I        3977.0169   194   8342.0338     8.9488      0.0038    0.9746
TVMef+G      3978.3243   193   8342.6487     9.5637      0.0028    0.9774
TIM2+G       3976.4322   195   8342.8644     9.7794      0.0025    0.9799
TIM3+G       3976.5195   195   8343.0390     9.9540      0.0023    0.9822
TrNef+I+G    3979.6235   192   8343.2469    10.1619      0.0021    0.9842
TVMef+I      3978.6416   193   8343.2833    10.1983      0.0020    0.9862
TIM3ef+I+G   3978.8987   193   8343.7974    10.7124      0.0016    0.9878
TIM2ef+I+G   3979.0369   193   8344.0738    10.9888      0.0014    0.9891
TIM2+I       3977.1131   195   8344.2261    11.1411      0.0013    0.9904
TPM2uf+I+G   3977.1681   195   8344.3363    11.2513      0.0012    0.9916
TIM3+I       3977.2328   195   8344.4657    11.3807      0.0011    0.9927
TPM3uf+I+G   3977.2722   195   8344.5444    11.4594      0.0011    0.9938
TrNef+G      3981.4667   191   8344.9334    11.8484      0.0009    0.9947
TPM2uf+G     3978.8367   194   8345.6733    12.5883      0.0006    0.9953
TIM2ef+G     3980.9165   192   8345.8330    12.7480      0.0006    0.9958
TPM3uf+G     3978.9355   194   8345.8710    12.7860      0.0006    0.9964
TrNef+I      3982.0141   191   8346.0281    12.9431      0.0005    0.9969
TPM2+I+G     3981.0631   192   8346.1262    13.0412      0.0005    0.9974
TPM2uf+I     3979.2376   194   8346.4753    13.3903      0.0004    0.9978
TPM3uf+I     3979.3623   194   8346.7245    13.6395      0.0004    0.9982
TIM3ef+G     3981.4053   192   8346.8105    13.7255      0.0003    0.9985
TIM2ef+I     3981.4634   192   8346.9268    13.8418      0.0003    0.9988
TPM3+I+G     3981.5399   192   8347.0798    13.9948      0.0003    0.9991
TPM2+G       3982.7672   191   8347.5345    14.4495      0.0002    0.9994
TIM3ef+I     3981.9660   192   8347.9321    14.8471      0.0002    0.9996
TPM2+I       3983.0846   191   8348.1691    15.0841      0.0002    0.9997
TPM3+G       3983.2694   191   8348.5387    15.4537      0.0001    0.9999
TPM3+I       3983.5987   191   8349.1974    16.1124      0.0001    1.0000
TrN+G        3986.5062   194   8361.0124    27.9274   2.85e-007    1.0000
TrN+I+G      3985.9135   195   8361.8270    28.7420   1.90e-007    1.0000
K80+G        4002.7645   190   8385.5289    52.4439   1.35e-012    1.0000
TrN+I        4007.9672   194   8403.9345    70.8495   1.36e-016    1.0000
HKY+I        4012.6695   193   8411.3390    78.2540   3.36e-018    1.0000
K80+I        4017.0481   190   8414.0961    81.0111   8.47e-019    1.0000
K80+I+G      4023.3754   191   8428.7508    95.6658   5.57e-022    1.0000
HKY+G        4025.3362   193   8436.6724   103.5874   1.06e-023    1.0000
HKY+I+G      4029.0376   194   8446.0753   112.9903   9.63e-026    1.0000
TIM1         4038.8977   194   8465.7954   132.7104   5.03e-030    1.0000
GTR          4038.5078   196   8469.0155   135.9305   1.01e-030    1.0000
TIM1ef       4045.1828   191   8472.3657   139.2807   1.88e-031    1.0000
TrN          4043.3488   193   8472.6977   139.6127   1.60e-031    1.0000
TPM1uf       4043.3657   193   8472.7313   139.6463   1.57e-031    1.0000
TIM3         4042.8344   194   8473.6687   140.5837   9.82e-032    1.0000
TIM2         4043.0816   194   8474.1633   141.0783   7.67e-032    1.0000
SYM          4044.6686   193   8475.3373   142.2523   4.26e-032    1.0000
TVM          4042.9772   195   8475.9544   142.8694   3.13e-032    1.0000
TPM1         4048.9682   190   8477.9363   144.8513   1.16e-032    1.0000
TrNef        4049.5106   190   8479.0212   145.9362   6.75e-033    1.0000
TIM2ef       4049.1330   191   8480.2660   147.1810   3.63e-033    1.0000
TIM3ef       4049.2842   191   8480.5685   147.4835   3.12e-033    1.0000
TPM3uf       4047.3027   193   8480.6053   147.5203   3.06e-033    1.0000
TVMef        4048.4548   192   8480.9095   147.8245   2.63e-033    1.0000
TPM2uf       4047.5481   193   8481.0962   148.0112   2.39e-033    1.0000
TPM2         4052.9171   190   8485.8342   152.7492   2.24e-034    1.0000
TPM3         4053.0684   190   8486.1369   153.0519   1.93e-034    1.0000
K80          4087.1188   189   8552.2377   219.1527   8.53e-049    1.0000
HKY          4094.9308   192   8573.8616   240.7766   1.72e-053    1.0000
F81+I+G      4157.5227   193   8701.0454   367.9604   4.15e-081    1.0000
F81+G        4159.1537   192   8702.3074   369.2224   2.21e-081    1.0000
F81+I        4159.5220   192   8703.0439   369.9589   1.53e-081    1.0000
JC+I+G       4161.8564   190   8703.7128   370.6278   1.09e-081    1.0000
JC+G         4163.4949   189   8704.9897   371.9047   5.77e-082    1.0000
JC+I         4163.6129   189   8705.2259   372.1409   5.13e-082    1.0000
F81          4228.2212   191   8838.4423   505.3573   6.06e-111    1.0000
JC           4232.9421   188   8841.8843   508.7993   1.08e-111    1.0000
------------------------------------------------------------------------

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[Aron]

What is your application called? I'm also having a difficult time implementing the TIM2+I+G model.  BEAST will not let me add an additional rate parameter.

I would like to include the following parameters:

 freqA = 0.3383 

   freqC = 0.1718 

   freqG = 0.0827 

   freqT = 0.4072 

   R(a) [AC] =  0.6109

   R(b) [AG] =  7.4295

   R(c) [AT] =  0.6109

   R(d) [CG] =  1.0000

   R(e) [CT] =  6.4079

   R(f) [GT] =  1.0000

   p-inv = 0.4830

   gamma shape = 0.5550 

Any help much appreciated!

Aron @ UIUC