Web document 7.7. Output file from the ModelTest program in which 56 models of nucleotide substitution were evaluated.

 

The input consisted of 11 myoglobin coding sequences that were first executed using PAUP software.

 

Testing models of evolution - Modeltest 3.7

(c) Copyright, 1998-2005 David Posada  (dposada@uvigo.es)

Facultad de Biologia, Universidad de Vigo,

Campus Universitario, 36310 Vigo, Spain

_______________________________________________________________

Thu Jul 26 11:12:11 2007

OS = Macintosh (Sioux console)

Input format: PAUP* scores file

Run settings:

  Using the standard AIC (not the AICc)

  Not using branch lengths as parameters

  Including all models in model-averaging calculations

---------------------------------------------------------------

*                                                             *

*         HIERARCHICAL LIKELIHOD RATIO TESTS (hLRTs)          *

*                                                             *

---------------------------------------------------------------

Confidence level = 0.01

 Equal base frequencies

   Null model = JC                          -lnL0 = 2343.2463

   Alternative model = F81            -lnL1 = 2337.7295

   2(lnL1-lnL0) =   11.0337               df = 3

   P-value =  0.011545

 Ti=Tv

   Null model = JC                          -lnL0 = 2343.2463

   Alternative model = K80            -lnL1 = 2306.5754

   2(lnL1-lnL0) =   73.3418               df = 1

   P-value = <0.000001

 Equal Ti rates

   Null model = K80                         -lnL0 = 2306.5754

   Alternative model = TrNef          -lnL1 = 2303.4163

   2(lnL1-lnL0) =    6.3184               df = 1

   P-value =  0.011949

 Equal Tv rates

   Null model = K80                         -lnL0 = 2306.5754

   Alternative model = K81            -lnL1 = 2306.3589

   2(lnL1-lnL0) =    0.4331               df = 1

   P-value =  0.510469

 Equal rates among sites

   Null model = K80                         -lnL0 = 2306.5754

   Alternative model = K80+G          -lnL1 = 2242.7925

   2(lnL1-lnL0) =  127.5659               df = 1

   Using mixed chi-square distribution

   P-value = <0.000001

 No Invariable sites

   Null model = K80+G                       -lnL0 = 2242.7925

   Alternative model = K80+I+G        -lnL1 = 2242.4980

   2(lnL1-lnL0) =    0.5889               df = 1

   Using mixed chi-square distribution

   P-value =  0.221429

 Model selected: K80+G

  -lnL  =   2242.7925

   K    =   2

   Base frequencies:

     Equal frequencies

   Substitution model:

    Ti/tv ratio = 1.5819

   Among-site rate variation

     Proportion of invariable sites = 0

     Variable sites (G)

      Gamma distribution shape parameter =      0.4545

--

PAUP* Commands Block: If you want to implement the previous estimates as likelihod settings in PAUP*, attach the next block of commands after the data in your PAUP file:

[!

Likelihood settings from best-fit model (K80+G) selected by hLRT in Modeltest 3.7 on Thu Jul 26 11:12:11 2007

]

BEGIN PAUP;

Lset  Base=equal  Nst=2  TRatio=1.5819  Rates=gamma  Shape=0.4545  Pinvar=0;

END;

--

---------------------------------------------------------------

*                                                             *

*             AKAIKE INFORMATION CRITERION (AIC)              *

*                                                             *

---------------------------------------------------------------

 Model selected: TrN+G

  -lnL  =   2228.6187

   K    =   6

   AIC  =   4469.2373

   Base frequencies:

     freqA =       0.2573

     freqC =       0.2642

     freqG =       0.2980

     freqT =       0.1805

   Substitution model:

     Rate matrix

     R(a) [A-C] =        1.0000

     R(b) [A-G] =        2.2635

     R(c) [A-T] =        1.0000

     R(d) [C-G] =        1.0000

     R(e) [C-T] =        5.0391

     R(f) [G-T] =        1.0000

   Among-site rate variation

     Proportion of invariable sites = 0

     Variable sites (G)

      Gamma distribution shape parameter =      0.4433

--

PAUP* Commands Block: If you want to implement the previous estimates as likelihod settings in PAUP*, attach the next block of commands after the data in your PAUP file:

[!

Likelihood settings from best-fit model (TrN+G) selected by AIC in Modeltest 3.7 on Thu Jul 26 11:12:11 2007

]

BEGIN PAUP;

Lset  Base=(0.2573 0.2642 0.2980)  Nst=6  Rmat=(1.0000 2.2635 1.0000 1.0000 5.0391)  Rates=gamma  Shape=0.4433  Pinvar=0;

END;

--

 * MODEL SELECTION UNCERTAINTY : Akaike Weights

Model             -lnL   K         AIC      delta     weight  cumWeight

-----------------------------------------------------------------------

TrN+G        2228.6187  6    4469.2373     0.0000     0.3517    0.3517

TrN+I+G      2228.1694  7    4470.3389     1.1016     0.2027    0.5544

TIM+G        2228.3206  7    4470.6411     1.4038     0.1743    0.7287

GTR+G        2226.8057  9    4471.6113     2.3740     0.1073    0.8360

TIM+I+G      2227.8782  8    4471.7563     2.5190     0.0998    0.9359

GTR+I+G      2226.4597  10    4472.9194     3.6821     0.0558    0.9916

HKY+G        2234.6826  5    4479.3652    10.1279     0.0022    0.9939

SYM+G        2234.2625  6    4480.5249    11.2876     0.0012    0.9951

HKY+I+G      2234.3298  6    4480.6597    11.4224     0.0012    0.9963

K81uf+G      2234.4517  6    4480.9033    11.6660     0.0010    0.9973

TVM+G        2232.9568  8    4481.9136    12.6763     0.0006    0.9979

SYM+I+G      2234.0093  7    4482.0186    12.7812     0.0006    0.9985

K81uf+I+G    2234.0986  7    4482.1973    12.9600     0.0005    0.9991

TVM+I+G      2232.6309  9    4483.2617    14.0244     0.0003    0.9994

TVMef+G      2237.3064  5    4484.6128    15.3755     0.0002    0.9995

TrN+I        2236.7471  6    4485.4941    16.2568     0.0001    0.9996

TVMef+I+G    2237.0334  6    4486.0669    16.8296   7.79e-05    0.9997

TrNef+G      2240.0940  3    4486.1880    16.9507   7.33e-05    0.9998

TIMef+G      2239.3413  4    4486.6826    17.4453   5.73e-05    0.9998

TIM+I        2236.6038  7    4487.2075    17.9702   4.41e-05    0.9999

TrNef+I+G    2239.8000  4    4487.6001    18.3628   3.62e-05    0.9999

TIMef+I+G    2239.0437  5    4488.0874    18.8501   2.84e-05    1.0000

K80+G        2242.7925  2    4489.5850    20.3477   1.34e-05    1.0000

K81+G        2242.0952  3    4490.1904    20.9531   9.91e-06    1.0000

GTR+I        2236.4111  9    4490.8223    21.5850   7.23e-06    1.0000

K80+I+G      2242.4980  3    4490.9961    21.7588   6.63e-06    1.0000

K81+I+G      2241.7944  4    4491.5889    22.3516   4.93e-06    1.0000

HKY+I        2244.0312  5    4498.0625    28.8252   1.94e-07    1.0000

K81uf+I      2243.9150  6    4499.8301    30.5928   8.00e-08    1.0000

TVM+I        2243.6582  8    4503.3164    34.0791   1.40e-08    1.0000

SYM+I        2247.6377  6    4507.2754    38.0381   1.93e-09    1.0000

TrNef+I      2250.9824  3    4507.9648    38.7275   1.37e-09    1.0000

TIMef+I      2250.3979  4    4508.7959    39.5586   9.04e-10    1.0000

TVMef+I      2250.3684  5    4510.7368    41.4995   3.42e-10    1.0000

K80+I        2253.7705  2    4511.5410    42.3037   2.29e-10    1.0000

K81+I        2253.2083  3    4512.4165    43.1792   1.48e-10    1.0000

F81+G        2278.2764  4    4564.5527    95.3154   7.06e-22    1.0000

F81+I+G      2278.0466  5    4566.0933    96.8560   3.27e-22    1.0000

JC+G         2284.4009  1    4570.8018  101.5645   3.10e-23    1.0000

JC+I+G       2284.1919  2    4572.3838  103.1465   1.41e-23    1.0000

F81+I        2287.1672  4    4582.3345  113.0972   9.71e-26    1.0000

JC+I         2294.1985  1    4590.3970  121.1597   1.72e-27    1.0000

GTR          2289.9819  8    4595.9639  126.7266   1.07e-28    1.0000

TrN          2294.6165  5    4599.2329  129.9956   2.08e-29    1.0000

TIM          2294.4741  6    4600.9482  131.7109   8.82e-30    1.0000

SYM          2295.6414  5    4601.2827  132.0454   7.46e-30    1.0000

TVMef        2298.7981  4    4605.5962  136.3589   8.63e-31    1.0000

TVM          2296.5637  7    4607.1274  137.8901   4.02e-31    1.0000

HKY          2301.3118  4    4610.6235  141.3862   6.99e-32    1.0000

TrNef        2303.4163  2    4610.8325  141.5952   6.30e-32    1.0000

K81uf        2301.1807  5    4612.3613  143.1240   2.93e-32    1.0000

TIMef        2303.1917  3    4612.3833  143.1460   2.90e-32    1.0000

K80          2306.5754  1    4615.1509  145.9136   7.27e-33    1.0000

K81          2306.3589  2    4616.7178  147.4805   3.32e-33    1.0000

F81          2337.7295  3    4681.4590  212.2217   0.00e+00    1.0000

JC           2343.2463  0    4686.4927  217.2554   0.00e+00    1.0000

-----------------------------------------------------------------------

-lnL:       Negative log likelihod

 K:               Number of estimated parameters

 IC:        Information Criterion

 delta:           Information difference

 weight:    Information weight

 cumWeight: Cumulative information weight

* MODEL AVERAGING AND PARAMETER IMPORTANCE (using Akaike Weights)

  Including all 56 models

                         Model-averaged

Parameter   Importance        estimates

---------------------------------------

fA                      0.9977                 0.2582

fC                      0.9977                 0.2626

fG                      0.9977                 0.2972

fT                      0.9977                 0.1820

TiTv              0.0034                 1.6297

rAC                     0.1661                 1.4251

rAG                     0.9938                 2.4551

rAT                     0.1661                 0.9237

rCG                     0.1661                 1.7305

rCT                     0.9938                 5.4920

pinv(I)                 0.0002                 0.4778

alpha(G)          0.6387                 0.4442

pinv(IG)          0.3611                 0.2031

alpha(IG)         0.3611                 0.7231

---------------------------------------

 Values have been rounded.

 (I):       averaged using only +I models.

 (G):       averaged using only +G models.

 (IG):            averaged using only +I+G models.

_________________________________________________________________

Program is done.

Time processing: 0.03137 seconds

If you need help type '-?' in the command line of the program.