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 _______________________________________________________________ Mon Dec 19 19:18:00 2005 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 = 10760.4326 Alternative model = F81 -lnL1 = 10743.0303 2(lnL1-lnL0) = 34.8047 df = 3 P-value = <0.000001 Ti=Tv Null model = F81 -lnL0 = 10743.0303 Alternative model = HKY -lnL1 = 10513.0137 2(lnL1-lnL0) = 460.0332 df = 1 P-value = <0.000001 Equal Ti rates Null model = HKY -lnL0 = 10513.0137 Alternative model = TrN -lnL1 = 10511.7031 2(lnL1-lnL0) = 2.6211 df = 1 P-value = 0.105452 Equal Tv rates Null model = HKY -lnL0 = 10513.0137 Alternative model = K81uf -lnL1 = 10512.6514 2(lnL1-lnL0) = 0.7246 df = 1 P-value = 0.394636 Equal rates among sites Null model = HKY -lnL0 = 10513.0137 Alternative model = HKY+G -lnL1 = 9842.9697 2(lnL1-lnL0) = 1340.0879 df = 1 Using mixed chi-square distribution P-value = <0.000001 No Invariable sites Null model = HKY+G -lnL0 = 9842.9697 Alternative model = HKY+I+G -lnL1 = 9827.4727 2(lnL1-lnL0) = 30.9941 df = 1 Using mixed chi-square distribution P-value = <0.000001 Model selected: HKY+I+G -lnL = 9827.4727 K = 6 Base frequencies: freqA = 0.2026 freqC = 0.3147 freqG = 0.2909 freqT = 0.1918 Substitution model: Ti/tv ratio = 1.6307 Among-site rate variation Proportion of invariable sites (I) = 0.1916 Variable sites (G) Gamma distribution shape parameter = 1.2661 -- 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 Mon Dec 19 19:18:00 2005 ] BEGIN PAUP; Lset Base=(0.2026 0.3147 0.2909) Nst=2 TRatio=1.6307 Rates=gamma Shape=1.2661 Pinvar=0.1916; END; -- --------------------------------------------------------------- * * * AKAIKE INFORMATION CRITERION (AIC) * * * --------------------------------------------------------------- Model selected: TVM+I+G -lnL = 9815.3438 K = 9 AIC = 19648.6875 Base frequencies: freqA = 0.1926 freqC = 0.2915 freqG = 0.3057 freqT = 0.2102 Substitution model: Rate matrix R(a) [A-C] = 2.2397 R(b) [A-G] = 5.2825 R(c) [A-T] = 1.2748 R(d) [C-G] = 1.6492 R(e) [C-T] = 5.2825 R(f) [G-T] = 1.0000 Among-site rate variation Proportion of invariable sites (I) = 0.1847 Variable sites (G) Gamma distribution shape parameter = 1.2272 -- 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 (TVM+I+G) selected by AIC in Modeltest 3.7 on Mon Dec 19 19:18:00 2005 ] BEGIN PAUP; Lset Base=(0.1926 0.2915 0.3057) Nst=6 Rmat=(2.2397 5.2825 1.2748 1.6492 5.2825) Rates=gamma Shape=1.2272 Pinvar=0.1847; END; -- * MODEL SELECTION UNCERTAINTY : Akaike Weights Model -lnL K AIC delta weight cumWeight ------------------------------------------------------------------------------------------------- TVM+I+G 9815.3438 9 19648.6875 0.0000 0.6237 0.6237 GTR+I+G 9814.8496 10 19649.6992 1.0117 0.3761 0.9998 TrN+I+G 9826.1738 7 19666.3477 17.6602 9.12e-05 0.9999 HKY+I+G 9827.4727 6 19666.9453 18.2578 6.77e-05 0.9999 TIM+I+G 9826.0967 8 19668.1934 19.5059 3.63e-05 1.0000 K81uf+I+G 9827.4141 7 19668.8281 20.1406 2.64e-05 1.0000 TVM+G 9827.9150 8 19671.8301 23.1426 5.88e-06 1.0000 GTR+G 9827.6787 9 19673.3574 24.6699 2.74e-06 1.0000 HKY+G 9842.9697 5 19695.9395 47.2520 3.42e-11 1.0000 TrN+G 9842.1006 6 19696.2012 47.5137 3.00e-11 1.0000 K81uf+G 9842.9473 6 19697.8945 49.2070 1.29e-11 1.0000 TIM+G 9842.0625 7 19698.1250 49.4375 1.15e-11 1.0000 SYM+I+G 9846.3066 7 19706.6133 57.9258 1.65e-13 1.0000 TVMef+I+G 9847.4277 6 19706.8555 58.1680 1.46e-13 1.0000 TVMef+G 9856.4043 5 19722.8086 74.1211 5.01e-17 1.0000 SYM+G 9855.4121 6 19722.8242 74.1367 4.97e-17 1.0000 K81+I+G 9885.7041 4 19779.4082 130.7207 2.57e-29 1.0000 TIMef+I+G 9885.0508 5 19780.1016 131.4141 1.81e-29 1.0000 K80+I+G 9887.3311 3 19780.6621 131.9746 1.37e-29 1.0000 TrNef+I+G 9886.6328 4 19781.2656 132.5781 1.01e-29 1.0000 K81+G 9897.6230 3 19801.2461 152.5586 4.65e-34 1.0000 TIMef+G 9897.1484 4 19802.2969 153.6094 2.75e-34 1.0000 K80+G 9899.2500 2 19802.5000 153.8125 2.48e-34 1.0000 TrNef+G 9898.7275 3 19803.4551 154.7676 1.54e-34 1.0000 GTR+I 10055.6943 9 20129.3887 480.7012 0.00e+00 1.0000 TVM+I 10058.2002 8 20132.4004 483.7129 0.00e+00 1.0000 TrN+I 10064.3848 6 20140.7695 492.0820 0.00e+00 1.0000 TIM+I 10064.3838 7 20142.7676 494.0801 0.00e+00 1.0000 HKY+I 10067.5029 5 20145.0059 496.3184 0.00e+00 1.0000 K81uf+I 10067.5029 6 20147.0059 498.3184 0.00e+00 1.0000 SYM+I 10091.9834 6 20195.9668 547.2793 0.00e+00 1.0000 TVMef+I 10094.3945 5 20198.7891 550.1016 0.00e+00 1.0000 F81+I+G 10105.6084 5 20221.2168 572.5293 0.00e+00 1.0000 F81+G 10118.0361 4 20244.0723 595.3848 0.00e+00 1.0000 TIMef+I 10119.7910 4 20247.5820 598.8945 0.00e+00 1.0000 TrNef+I 10121.6934 3 20249.3867 600.6992 0.00e+00 1.0000 K81+I 10122.2090 3 20250.4180 601.7305 0.00e+00 1.0000 K80+I 10124.1289 2 20252.2578 603.5703 0.00e+00 1.0000 JC+I+G 10135.4238 2 20274.8477 626.1602 0.00e+00 1.0000 JC+G 10146.4355 1 20294.8711 646.1836 0.00e+00 1.0000 F81+I 10321.2637 4 20650.5273 1001.8398 0.00e+00 1.0000 JC+I 10350.8770 1 20703.7539 1055.0664 0.00e+00 1.0000 TVM 10474.0742 7 20962.1484 1313.4609 0.00e+00 1.0000 GTR 10473.0889 8 20962.1777 1313.4902 0.00e+00 1.0000 SYM 10486.8154 5 20983.6309 1334.9434 0.00e+00 1.0000 TVMef 10489.1514 4 20986.3027 1337.6152 0.00e+00 1.0000 TrN 10511.7031 5 21033.4062 1384.7188 0.00e+00 1.0000 HKY 10513.0137 4 21034.0273 1385.3398 0.00e+00 1.0000 TIM 10511.3320 6 21034.6641 1385.9766 0.00e+00 1.0000 K81uf 10512.6514 5 21035.3027 1386.6152 0.00e+00 1.0000 TIMef 10540.5850 3 21087.1699 1438.4824 0.00e+00 1.0000 TrNef 10542.4160 2 21088.8320 1440.1445 0.00e+00 1.0000 K81 10542.5566 2 21089.1133 1440.4258 0.00e+00 1.0000 K80 10544.3965 1 21090.7930 1442.1055 0.00e+00 1.0000 F81 10743.0303 3 21492.0605 1843.3730 0.00e+00 1.0000 JC 10760.4326 0 21520.8652 1872.1777 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 0.1945 fC 1.0000 0.2896 fG 1.0000 0.3079 fT 1.0000 0.2080 TiTv 0.0001 1.6307 rAC 0.9998 2.2200 rAG 0.3762 4.8779 rAT 0.9998 1.2647 rCG 0.9998 1.6435 rCT 0.3762 5.5650 pinv(I) 0.0000 - alpha(G) 0.0000 0.6392 pinv(IG) 1.0000 0.1851 alpha(IG) 1.0000 1.2305 --------------------------------------- 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: 0.013 seconds If you need help type '-?' in the command line of the program.