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 _______________________________________________________________ Sat Jul 22 05:23:37 2006 OS = Windows Input format: PAUP* scores file Run settings: Using the BIC sample size = 705 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 = 5197.7739 Alternative model = F81 -lnL1 = 5131.3843 2(lnL1-lnL0) = 132.7793 df = 3 P-value = <0.000001 Ti=Tv Null model = F81 -lnL0 = 5131.3843 Alternative model = HKY -lnL1 = 5049.1602 2(lnL1-lnL0) = 164.4482 df = 1 P-value = <0.000001 Equal Ti rates Null model = HKY -lnL0 = 5049.1602 Alternative model = TrN -lnL1 = 5047.0806 2(lnL1-lnL0) = 4.1592 df = 1 P-value = 0.041409 Equal Tv rates Null model = HKY -lnL0 = 5049.1602 Alternative model = K81uf -lnL1 = 5046.6387 2(lnL1-lnL0) = 5.0430 df = 1 P-value = 0.024726 Equal rates among sites Null model = HKY -lnL0 = 5049.1602 Alternative model = HKY+G -lnL1 = 4714.6235 2(lnL1-lnL0) = 669.0732 df = 1 Using mixed chi-square distribution P-value = <0.000001 No Invariable sites Null model = HKY+G -lnL0 = 4714.6235 Alternative model = HKY+I+G -lnL1 = 4710.6982 2(lnL1-lnL0) = 7.8506 df = 1 Using mixed chi-square distribution P-value = 0.002540 Model selected: HKY+I+G -lnL = 4710.6982 K = 6 Base frequencies: freqA = 0.3457 freqC = 0.3071 freqG = 0.1036 freqT = 0.2435 Substitution model: Ti/tv ratio = 2.7720 Among-site rate variation Proportion of invariable sites (I) = 0.2100 Variable sites (G) Gamma distribution shape parameter = 0.4677 -- 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 (HKY+I+G) selected by hLRT in Modeltest 3.7 on Sat Jul 22 05:23:37 2006 ] BEGIN PAUP; Lset Base=(0.3457 0.3071 0.1036) Nst=2 TRatio=2.7720 Rates=gamma Shape=0.4677 Pinvar=0.2100; END; -- --------------------------------------------------------------- * * * BAYESIAN INFORMATION CRITERION (BIC) * * * --------------------------------------------------------------- Model selected: HKY+I+G -lnL = 4710.6982 K = 6 BIC = 9460.7461 Base frequencies: freqA = 0.3457 freqC = 0.3071 freqG = 0.1036 freqT = 0.2435 Substitution model: Ti/tv ratio = 2.7720 Among-site rate variation Proportion of invariable sites (I) = 0.2100 Variable sites (G) Gamma distribution shape parameter = 0.4677 -- 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 (HKY+I+G) selected by BIC in Modeltest 3.7 on Sat Jul 22 05:23:37 2006 ] BEGIN PAUP; Lset Base=(0.3457 0.3071 0.1036) Nst=2 TRatio=2.7720 Rates=gamma Shape=0.4677 Pinvar=0.2100; END; -- * MODEL SELECTION UNCERTAINTY : BIC Weights (approximate posterior probabilities) Model -lnL K BIC delta weight cumWeight ----------------------------------------------------------------------------------------------------- HKY+I+G 4710.6982 6 9460.7461 0.0000 0.3374 0.3374 TrN+I+G 4707.7842 7 9461.4756 0.7295 0.2343 0.5716 TrN+G 4711.1958 6 9461.7412 0.9951 0.2051 0.7768 HKY+G 4714.6235 5 9462.0381 1.2920 0.1768 0.9536 K81uf+I+G 4710.4448 7 9466.7969 6.0508 0.0164 0.9700 TIM+I+G 4707.5327 8 9467.5312 6.7852 0.0113 0.9813 TIM+G 4710.9233 7 9467.7539 7.0078 0.0101 0.9914 K81uf+G 4714.4004 6 9468.1504 7.4043 0.0083 0.9998 GTR+I+G 4705.5688 10 9476.7197 15.9736 0.0001 0.9999 GTR+G 4709.5698 9 9478.1631 17.4170 5.57e-05 0.9999 TVM+I+G 4709.8530 9 9478.7295 17.9834 4.20e-05 1.0000 TVM+G 4713.9624 8 9480.3906 19.6445 1.83e-05 1.0000 SYM+G 4762.0713 6 9563.4922 102.7461 1.65e-23 1.0000 SYM+I+G 4758.8462 7 9563.5996 102.8535 1.56e-23 1.0000 GTR+I 4756.8589 9 9572.7412 111.9951 1.62e-25 1.0000 TVM+I 4761.1963 8 9574.8584 114.1123 5.61e-26 1.0000 HKY+I 4774.9268 5 9582.6445 121.8984 1.14e-27 1.0000 TrN+I 4773.1138 6 9585.5771 124.8311 2.64e-28 1.0000 K81uf+I 4774.8740 6 9589.0977 128.3516 4.54e-29 1.0000 TIM+I 4773.0552 7 9592.0176 131.2715 1.05e-29 1.0000 SYM+I 4791.9551 6 9623.2598 162.5137 1.73e-36 1.0000 TVMef+G 4797.2412 5 9627.2734 166.5273 2.33e-37 1.0000 TVMef+I+G 4795.0786 6 9629.5068 168.7607 7.62e-38 1.0000 TrNef+G 4817.3774 3 9654.4297 193.6836 2.96e-43 1.0000 TrNef+I+G 4814.4189 4 9655.0703 194.3242 2.14e-43 1.0000 TIMef+G 4815.3486 4 9656.9297 196.1836 8.41e-44 1.0000 TIMef+I+G 4812.3179 5 9657.4268 196.6807 6.59e-44 1.0000 TVMef+I 4828.2070 5 9689.2051 228.4590 0.00e+00 1.0000 TIMef+I 4853.5029 4 9733.2383 272.4922 0.00e+00 1.0000 TrNef+I 4856.9751 3 9733.6250 272.8789 0.00e+00 1.0000 K80+G 4862.7222 2 9738.5605 277.8145 0.00e+00 1.0000 K80+I+G 4859.6572 3 9738.9893 278.2432 0.00e+00 1.0000 K81+G 4860.2822 3 9740.2393 279.4932 0.00e+00 1.0000 K81+I+G 4857.1812 4 9740.5947 279.8486 0.00e+00 1.0000 F81+G 4860.0811 4 9746.3945 285.6484 0.00e+00 1.0000 F81+I+G 4857.2520 5 9747.2949 286.5488 0.00e+00 1.0000 K81+I 4889.1226 3 9797.9199 337.1738 0.00e+00 1.0000 K80+I 4892.5742 2 9798.2646 337.5186 0.00e+00 1.0000 F81+I 4888.9883 4 9804.2090 343.4629 0.00e+00 1.0000 JC+G 4953.2383 1 9913.0352 452.2891 0.00e+00 1.0000 JC+I+G 4950.1587 2 9913.4336 452.6875 0.00e+00 1.0000 JC+I 4972.3730 1 9951.3047 490.5586 0.00e+00 1.0000 TVM 4998.7012 7 10043.3096 582.5635 0.00e+00 1.0000 GTR 4995.7231 8 10043.9121 583.1660 0.00e+00 1.0000 SYM 5011.2847 5 10055.3604 594.6143 0.00e+00 1.0000 TVMef 5033.3145 4 10092.8613 632.1152 0.00e+00 1.0000 HKY 5049.1602 4 10124.5527 663.8066 0.00e+00 1.0000 K81uf 5046.6387 5 10126.0684 665.3223 0.00e+00 1.0000 TrN 5047.0806 5 10126.9521 666.2061 0.00e+00 1.0000 TIM 5044.5513 6 10128.4521 667.7061 0.00e+00 1.0000 TIMef 5096.9717 3 10213.6182 752.8721 0.00e+00 1.0000 TrNef 5100.2681 2 10213.6523 752.9062 0.00e+00 1.0000 K80 5125.0405 1 10256.6396 795.8936 0.00e+00 1.0000 K81 5121.8086 2 10256.7334 795.9873 0.00e+00 1.0000 F81 5131.3843 3 10282.4434 821.6973 0.00e+00 1.0000 JC 5197.7739 0 10395.5479 934.8018 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 BIC weights) Including all 56 models Model-averaged Parameter Importance estimates --------------------------------------- fA 1.0000 0.3527 fC 1.0000 0.3018 fG 1.0000 0.1070 fT 1.0000 0.2385 TiTv 0.5142 2.8551 rAC 0.0002 1.0018 rAG 0.4610 4.8374 rAT 0.0002 1.5041 rCG 0.0002 0.6564 rCT 0.4610 9.1010 pinv(I) 0.0000 0.4154 alpha(G) 0.4005 0.2775 pinv(IG) 0.5995 0.2012 alpha(IG) 0.5995 0.4468 --------------------------------------- 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: 0.007 seconds If you need help type '-?' in the command line of the program.