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 05:23:25 2006 OS = Windows Input format: PAUP* scores file Run settings: Using the AICc correction 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 05:23:25 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; -- --------------------------------------------------------------- * * * CORRECTED AKAIKE INFORMATION CRITERION (AICc) * * * --------------------------------------------------------------- Model selected: TrN+I+G -lnL = 4707.7842 K = 7 AICc = 9429.7295 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 AICc in Modeltest 3.7 on Sat Jul 22 05:23:25 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 AICc delta weight cumWeight ----------------------------------------------------------------------------------------------------- TrN+I+G 4707.7842 7 9429.7295 0.0000 0.4367 0.4367 TIM+I+G 4707.5327 8 9431.2725 1.5430 0.2019 0.6385 GTR+I+G 4705.5688 10 9431.4551 1.7256 0.1843 0.8228 HKY+I+G 4710.6982 6 9433.5166 3.7871 0.0657 0.8885 TrN+G 4711.1958 6 9434.5117 4.7822 0.0400 0.9285 K81uf+I+G 4710.4448 7 9435.0508 5.3213 0.0305 0.9590 TIM+G 4710.9233 7 9436.0078 6.2783 0.0189 0.9779 GTR+G 4709.5698 9 9437.3984 7.6689 0.0094 0.9874 TVM+I+G 4709.8530 9 9437.9648 8.2354 0.0071 0.9945 HKY+G 4714.6235 5 9439.3330 9.6035 0.0036 0.9981 K81uf+G 4714.4004 6 9440.9209 11.1914 0.0016 0.9997 TVM+G 4713.9624 8 9444.1318 14.4023 0.0003 1.0000 SYM+I+G 4758.8462 7 9531.8535 102.1240 2.91e-23 1.0000 GTR+I 4756.8589 9 9531.9766 102.2471 2.74e-23 1.0000 SYM+G 4762.0713 6 9536.2627 106.5332 3.21e-24 1.0000 TVM+I 4761.1963 8 9538.5996 108.8701 9.98e-25 1.0000 TrN+I 4773.1138 6 9558.3477 128.6182 5.14e-29 1.0000 HKY+I 4774.9268 5 9559.9395 130.2100 2.32e-29 1.0000 TIM+I 4773.0552 7 9560.2715 130.5420 1.96e-29 1.0000 K81uf+I 4774.8740 6 9561.8682 132.1387 8.84e-30 1.0000 SYM+I 4791.9551 6 9596.0303 166.3008 3.38e-37 1.0000 TVMef+I+G 4795.0786 6 9602.2773 172.5479 1.49e-38 1.0000 TVMef+G 4797.2412 5 9604.5684 174.8389 4.72e-39 1.0000 TIMef+I+G 4812.3179 5 9634.7217 204.9922 1.40e-45 1.0000 TrNef+I+G 4814.4189 4 9636.8955 207.1660 0.00e+00 1.0000 TIMef+G 4815.3486 4 9638.7549 209.0254 0.00e+00 1.0000 TrNef+G 4817.3774 3 9640.7891 211.0596 0.00e+00 1.0000 TVMef+I 4828.2070 5 9666.5000 236.7705 0.00e+00 1.0000 TIMef+I 4853.5029 4 9715.0635 285.3340 0.00e+00 1.0000 TrNef+I 4856.9751 3 9719.9844 290.2549 0.00e+00 1.0000 K81+I+G 4857.1812 4 9722.4199 292.6904 0.00e+00 1.0000 F81+I+G 4857.2520 5 9724.5898 294.8604 0.00e+00 1.0000 K80+I+G 4859.6572 3 9725.3486 295.6191 0.00e+00 1.0000 K81+G 4860.2822 3 9726.5986 296.8691 0.00e+00 1.0000 F81+G 4860.0811 4 9728.2197 298.4902 0.00e+00 1.0000 K80+G 4862.7222 2 9729.4619 299.7324 0.00e+00 1.0000 K81+I 4889.1226 3 9784.2793 354.5498 0.00e+00 1.0000 F81+I 4888.9883 4 9786.0342 356.3047 0.00e+00 1.0000 K80+I 4892.5742 2 9789.1660 359.4365 0.00e+00 1.0000 JC+I+G 4950.1587 2 9904.3350 474.6055 0.00e+00 1.0000 JC+G 4953.2383 1 9908.4824 478.7529 0.00e+00 1.0000 JC+I 4972.3730 1 9946.7520 517.0225 0.00e+00 1.0000 GTR 4995.7231 8 10007.6533 577.9238 0.00e+00 1.0000 TVM 4998.7012 7 10011.5635 581.8340 0.00e+00 1.0000 SYM 5011.2847 5 10032.6553 602.9258 0.00e+00 1.0000 TVMef 5033.3145 4 10074.6865 644.9570 0.00e+00 1.0000 TIM 5044.5513 6 10101.2227 671.4932 0.00e+00 1.0000 K81uf 5046.6387 5 10103.3633 673.6338 0.00e+00 1.0000 TrN 5047.0806 5 10104.2471 674.5176 0.00e+00 1.0000 HKY 5049.1602 4 10106.3779 676.6484 0.00e+00 1.0000 TIMef 5096.9717 3 10199.9775 770.2480 0.00e+00 1.0000 TrNef 5100.2681 2 10204.5537 774.8242 0.00e+00 1.0000 K81 5121.8086 2 10247.6348 817.9053 0.00e+00 1.0000 K80 5125.0405 1 10252.0869 822.3574 0.00e+00 1.0000 F81 5131.3843 3 10268.8027 839.0732 0.00e+00 1.0000 JC 5197.7739 0 10395.5479 965.8184 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 AICc weights) Including all 56 models Model-averaged Parameter Importance estimates --------------------------------------- fA 1.0000 0.3554 fC 1.0000 0.2992 fG 1.0000 0.1122 fT 1.0000 0.2332 TiTv 0.0693 2.7846 rAC 0.2011 1.0857 rAG 0.8911 4.8262 rAT 0.2011 1.6374 rCG 0.2011 0.6164 rCT 0.8911 9.0751 pinv(I) 0.0000 0.4147 alpha(G) 0.0739 0.2718 pinv(IG) 0.9261 0.1992 alpha(IG) 0.9261 0.4408 --------------------------------------- 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.