Testing models of evolution - Modeltest 3.5 (c) Copyright, 1998-2004 David Posada (dposada@uvigo.es) Facultad de Biologia, Universidad de Vigo, 36200 Vigo, Spain _______________________________________________________________ Tue Apr 21 10:40:08 2009 OS = Unix-like Input format: Paup matrix file ** Log Likelihood scores ** +I +G +I+G JC = 2670.1055 2661.3025 2661.1252 2661.0691 F81 = 2664.0874 2655.4885 2655.2986 2655.2429 K80 = 2645.9841 2636.9717 2636.7200 2636.6260 HKY = 2639.6880 2630.8892 2630.6167 2630.5242 TrNef = 2641.6731 2633.5957 2633.3008 2633.2266 TrN = 2634.2585 2626.5928 2626.2610 2626.1931 K81 = 2645.6179 2636.5464 2636.3013 2636.2100 K81uf = 2639.2959 2630.4575 2630.1892 2630.0986 TIMef = 2641.3174 2633.1863 2632.8955 2632.8223 TIM = 2633.8811 2626.1829 2625.8528 2625.7856 TVMef = 2644.0981 2635.1208 2634.8662 2634.7725 TVM = 2638.2466 2629.5518 2629.2827 2629.1960 SYM = 2639.8203 2631.7576 2631.4539 2631.3772 GTR = 2632.8440 2625.2378 2624.9072 2624.8420 ** Settings ** Using the standard AIC (not the AICc) Not using branch lengths as parameters ** Hierarchical Likelihood Ratio Tests (hLRTs) ** Equal base frequencies Null model = JC -lnL0 = 2670.1055 Alternative model = F81 -lnL1 = 2664.0874 2(lnL1-lnL0) = 12.0361 df = 3 P-value = 0.007260 Ti=Tv Null model = F81 -lnL0 = 2664.0874 Alternative model = HKY -lnL1 = 2639.6880 2(lnL1-lnL0) = 48.7988 df = 1 P-value = <0.000001 Equal Ti rates Null model = HKY -lnL0 = 2639.6880 Alternative model = TrN -lnL1 = 2634.2585 2(lnL1-lnL0) = 10.8589 df = 1 P-value = 0.000983 Equal Tv rates Null model = TrN -lnL0 = 2634.2585 Alternative model = TIM -lnL1 = 2633.8811 2(lnL1-lnL0) = 0.7549 df = 1 P-value = 0.384935 Equal rates among sites Null model = TrN -lnL0 = 2634.2585 Alternative model = TrN+G -lnL1 = 2626.2610 2(lnL1-lnL0) = 15.9951 df = 1 Using mixed chi-square distribution P-value = 0.000032 No Invariable sites Null model = TrN+G -lnL0 = 2626.2610 Alternative model = TrN+I+G -lnL1 = 2626.1931 2(lnL1-lnL0) = 0.1357 df = 1 Using mixed chi-square distribution P-value = 0.356276 Model selected: TrN+G -lnL = 2626.2610 K = 6 Base frequencies: freqA = 0.2729 freqC = 0.2102 freqG = 0.2476 freqT = 0.2693 Substitution model: Rate matrix R(a) [A-C] = 1.0000 R(b) [A-G] = 2.1644 R(c) [A-T] = 1.0000 R(d) [C-G] = 1.0000 R(e) [C-T] = 4.3389 R(f) [G-T] = 1.0000 Among-site rate variation Proportion of invariable sites = 0 Variable sites (G) Gamma distribution shape parameter = 0.3633 -- 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 hLRT in Modeltest 3.5 ] BEGIN PAUP; Lset Base=(0.2729 0.2102 0.2476) Nst=6 Rmat=(1.0000 2.1644 1.0000 1.0000 4.3389) Rates=gamma Shape=0.3633 Pinvar=0; END; -- ** Akaike Information Criterion (AIC) ** Model selected: TrN+G -lnL = 2626.2610 K = 6 AIC = 5264.5220 Base frequencies: freqA = 0.2729 freqC = 0.2102 freqG = 0.2476 freqT = 0.2693 Substitution model: Rate matrix R(a) [A-C] = 1.0000 R(b) [A-G] = 2.1644 R(c) [A-T] = 1.0000 R(d) [C-G] = 1.0000 R(e) [C-T] = 4.3389 R(f) [G-T] = 1.0000 Among-site rate variation Proportion of invariable sites = 0 Variable sites (G) Gamma distribution shape parameter = 0.3633 -- 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 3.5 ] BEGIN PAUP; Lset Base=(0.2729 0.2102 0.2476) Nst=6 Rmat=(1.0000 2.1644 1.0000 1.0000 4.3389) Rates=gamma Shape=0.3633 Pinvar=0; END; -- * Model selection uncertainty : Akaike Weights Model AIC Delta Weight CumWeight ---------------------------------------------------------- TrN+G 5264.5220 0.0000 0.2565 0.2565 TrN+I 5265.1855 0.6636 0.1841 0.4406 TIM+G 5265.7056 1.1836 0.1420 0.5826 TIM+I 5266.3657 1.8438 0.1020 0.6846 TrN+I+G 5266.3862 1.8643 0.1010 0.7856 TIM+I+G 5267.5713 3.0493 0.0558 0.8415 GTR+G 5267.8145 3.2925 0.0495 0.8910 GTR+I 5268.4756 3.9536 0.0355 0.9265 GTR+I+G 5269.6841 5.1621 0.0194 0.9459 HKY+G 5271.2334 6.7114 0.0089 0.9549 HKY+I 5271.7783 7.2563 0.0068 0.9617 K81uf+G 5272.3784 7.8564 0.0050 0.9667 TrNef+G 5272.6016 8.0796 0.0045 0.9712 K81uf+I 5272.9150 8.3931 0.0039 0.9751 HKY+I+G 5273.0483 8.5264 0.0036 0.9787 TrNef+I 5273.1914 8.6694 0.0034 0.9821 TIMef+G 5273.7910 9.2690 0.0025 0.9846 K81uf+I+G 5274.1973 9.6753 0.0020 0.9866 TIMef+I 5274.3726 9.8506 0.0019 0.9885 TrNef+I+G 5274.4531 9.9312 0.0018 0.9902 TVM+G 5274.5654 10.0435 0.0017 0.9919 SYM+G 5274.9077 10.3857 0.0014 0.9934 TVM+I 5275.1035 10.5815 0.0013 0.9947 SYM+I 5275.5151 10.9932 0.0011 0.9957 TIMef+I+G 5275.6445 11.1226 0.0010 0.9967 TVM+I+G 5276.3921 11.8701 0.0007 0.9974 SYM+I+G 5276.7544 12.2324 0.0006 0.9979 K80+G 5277.4399 12.9180 0.0004 0.9983 K80+I 5277.9434 13.4214 0.0003 0.9986 TrN 5278.5171 13.9951 0.0002 0.9989 K81+G 5278.6025 14.0806 0.0002 0.9991 K81+I 5279.0928 14.5708 0.0002 0.9993 K80+I+G 5279.2520 14.7300 0.0002 0.9994 TVMef+G 5279.7324 15.2104 0.0001 0.9996 TIM 5279.7622 15.2402 0.0001 0.9997 TVMef+I 5280.2417 15.7197 0.0001 0.9998 K81+I+G 5280.4199 15.8979 0.0001 0.9999 TVMef+I+G 5281.5449 17.0229 0.0001 0.9999 GTR 5281.6880 17.1660 0.0000 1.0000 TrNef 5287.3462 22.8242 0.0000 1.0000 HKY 5287.3760 22.8540 0.0000 1.0000 K81uf 5288.5918 24.0698 0.0000 1.0000 TIMef 5288.6348 24.1128 0.0000 1.0000 SYM 5289.6406 25.1187 0.0000 1.0000 TVM 5290.4932 25.9712 0.0000 1.0000 K80 5293.9683 29.4463 0.0000 1.0000 K81 5295.2358 30.7139 0.0000 1.0000 TVMef 5296.1963 31.6743 0.0000 1.0000 F81+G 5318.5972 54.0752 0.0000 1.0000 F81+I 5318.9771 54.4551 0.0000 1.0000 F81+I+G 5320.4858 55.9639 0.0000 1.0000 JC+G 5324.2505 59.7285 0.0000 1.0000 JC+I 5324.6050 60.0830 0.0000 1.0000 JC+I+G 5326.1382 61.6162 0.0000 1.0000 F81 5334.1748 69.6528 0.0000 1.0000 JC 5340.2109 75.6890 0.0000 1.0000 _________________________________________________________________ Time processing: 0 seconds If you need help type '-?' in the command line of the program