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 05:22:19 2006 OS = Windows 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 = 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 05:22:19 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; -- --------------------------------------------------------------- * * * AKAIKE INFORMATION CRITERION (AIC) * * * --------------------------------------------------------------- Model selected: TrN+I+G -lnL = 4707.7842 K = 7 AIC = 9429.5684 Base frequencies: freqA = 0.3578 freqC = 0.2972 freqG = 0.1114 freqT = 0.2336 Substitution model: Rate matrix R(a) [A-C] = 1.0000 R(b) [A-G] = 4.6646 R(c) [A-T] = 1.0000 R(d) [C-G] = 1.0000 R(e) [C-T] = 8.4075 R(f) [G-T] = 1.0000 Among-site rate variation Proportion of invariable sites (I) = 0.1887 Variable sites (G) Gamma distribution shape parameter = 0.4173 -- 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+I+G) selected by AIC in Modeltest 3.7 on Sat Jul 22 05:22:19 2006 ] BEGIN PAUP; Lset Base=(0.3578 0.2972 0.1114) Nst=6 Rmat=(1.0000 4.6646 1.0000 1.0000 8.4075) Rates=gamma Shape=0.4173 Pinvar=0.1887; END; -- * MODEL SELECTION UNCERTAINTY : Akaike Weights Model -lnL K AIC delta weight cumWeight -------------------------------------------------------------------------------------------------- TrN+I+G 4707.7842 7 9429.5684 0.0000 0.4289 0.4289 TIM+I+G 4707.5327 8 9431.0654 1.4971 0.2029 0.6317 GTR+I+G 4705.5688 10 9431.1377 1.5693 0.1957 0.8274 HKY+I+G 4710.6982 6 9433.3965 3.8281 0.0632 0.8906 TrN+G 4711.1958 6 9434.3916 4.8232 0.0385 0.9291 K81uf+I+G 4710.4448 7 9434.8896 5.3213 0.0300 0.9591 TIM+G 4710.9233 7 9435.8467 6.2783 0.0186 0.9777 GTR+G 4709.5698 9 9437.1396 7.5713 0.0097 0.9874 TVM+I+G 4709.8530 9 9437.7061 8.1377 0.0073 0.9947 HKY+G 4714.6235 5 9439.2471 9.6787 0.0034 0.9981 K81uf+G 4714.4004 6 9440.8008 11.2324 0.0016 0.9997 TVM+G 4713.9624 8 9443.9248 14.3564 0.0003 1.0000 SYM+I+G 4758.8462 7 9531.6924 102.1240 2.86e-23 1.0000 GTR+I 4756.8589 9 9531.7178 102.1494 2.82e-23 1.0000 SYM+G 4762.0713 6 9536.1426 106.5742 3.09e-24 1.0000 TVM+I 4761.1963 8 9538.3926 108.8242 1.00e-24 1.0000 TrN+I 4773.1138 6 9558.2275 128.6592 4.95e-29 1.0000 HKY+I 4774.9268 5 9559.8535 130.2852 2.19e-29 1.0000 TIM+I 4773.0552 7 9560.1104 130.5420 1.93e-29 1.0000 K81uf+I 4774.8740 6 9561.7480 132.1797 8.51e-30 1.0000 SYM+I 4791.9551 6 9595.9102 166.3418 3.25e-37 1.0000 TVMef+I+G 4795.0786 6 9602.1572 172.5889 1.43e-38 1.0000 TVMef+G 4797.2412 5 9604.4824 174.9141 4.47e-39 1.0000 TIMef+I+G 4812.3179 5 9634.6357 205.0674 1.40e-45 1.0000 TrNef+I+G 4814.4189 4 9636.8379 207.2695 0.00e+00 1.0000 TIMef+G 4815.3486 4 9638.6973 209.1289 0.00e+00 1.0000 TrNef+G 4817.3774 3 9640.7549 211.1865 0.00e+00 1.0000 TVMef+I 4828.2070 5 9666.4141 236.8457 0.00e+00 1.0000 TIMef+I 4853.5029 4 9715.0059 285.4375 0.00e+00 1.0000 TrNef+I 4856.9751 3 9719.9502 290.3818 0.00e+00 1.0000 K81+I+G 4857.1812 4 9722.3623 292.7939 0.00e+00 1.0000 F81+I+G 4857.2520 5 9724.5039 294.9355 0.00e+00 1.0000 K80+I+G 4859.6572 3 9725.3145 295.7461 0.00e+00 1.0000 K81+G 4860.2822 3 9726.5645 296.9961 0.00e+00 1.0000 F81+G 4860.0811 4 9728.1621 298.5938 0.00e+00 1.0000 K80+G 4862.7222 2 9729.4443 299.8760 0.00e+00 1.0000 K81+I 4889.1226 3 9784.2451 354.6768 0.00e+00 1.0000 F81+I 4888.9883 4 9785.9766 356.4082 0.00e+00 1.0000 K80+I 4892.5742 2 9789.1484 359.5801 0.00e+00 1.0000 JC+I+G 4950.1587 2 9904.3174 474.7490 0.00e+00 1.0000 JC+G 4953.2383 1 9908.4766 478.9082 0.00e+00 1.0000 JC+I 4972.3730 1 9946.7461 517.1777 0.00e+00 1.0000 GTR 4995.7231 8 10007.4463 577.8779 0.00e+00 1.0000 TVM 4998.7012 7 10011.4023 581.8340 0.00e+00 1.0000 SYM 5011.2847 5 10032.5693 603.0010 0.00e+00 1.0000 TVMef 5033.3145 4 10074.6289 645.0605 0.00e+00 1.0000 TIM 5044.5513 6 10101.1025 671.5342 0.00e+00 1.0000 K81uf 5046.6387 5 10103.2773 673.7090 0.00e+00 1.0000 TrN 5047.0806 5 10104.1611 674.5928 0.00e+00 1.0000 HKY 5049.1602 4 10106.3203 676.7520 0.00e+00 1.0000 TIMef 5096.9717 3 10199.9434 770.3750 0.00e+00 1.0000 TrNef 5100.2681 2 10204.5361 774.9678 0.00e+00 1.0000 K81 5121.8086 2 10247.6172 818.0488 0.00e+00 1.0000 K80 5125.0405 1 10252.0811 822.5127 0.00e+00 1.0000 F81 5131.3843 3 10268.7686 839.2002 0.00e+00 1.0000 JC 5197.7739 0 10395.5479 965.9795 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 1.0000 0.3554 fC 1.0000 0.2993 fG 1.0000 0.1123 fT 1.0000 0.2331 TiTv 0.0666 2.7843 rAC 0.2131 1.0860 rAG 0.8942 4.8239 rAT 0.2131 1.6380 rCG 0.2131 0.6162 rCT 0.8942 9.0870 pinv(I) 0.0000 0.4147 alpha(G) 0.0720 0.2719 pinv(IG) 0.9280 0.1997 alpha(IG) 0.9280 0.4418 --------------------------------------- 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: -0.002 seconds If you need help type '-?' in the command line of the program.