****Welcome to ModelGenerator v0.85**** If you use ModelGenerator in your analysis, please cite: Thomas M Keane, Christopher J Creevey , Melissa M Pentony, Thomas J Naughton and James O McInerney (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified, BMC Evolutionary Biology, 6:29 http://www.biomedcentral.com/1471-2148/6/29 Input sequence file: /home/gbottu/test/16SrRNA.fasta Format is FASTA Datatype is NUCLEOTIDE Building initial NJ tree...... Created models Starting to optimise model parameters..... Number of observed invariant sites: 1300 Optimising model 1 of 56: JC Optimising model 2 of 56: JC+G Optimising model 3 of 56: JC+I Optimising model 4 of 56: JC+I+G Optimising model 5 of 56: F81 Optimising model 6 of 56: F81+G Optimising model 7 of 56: F81+I Optimising model 8 of 56: F81+I+G Optimising model 9 of 56: HKY Optimising model 10 of 56: HKY+G Optimising model 11 of 56: HKY+I Optimising model 12 of 56: HKY+I+G Optimising model 13 of 56: K80 Optimising model 14 of 56: K80+G Optimising model 15 of 56: K80+I Optimising model 16 of 56: K80+I+G Optimising model 17 of 56: SYM Optimising model 18 of 56: SYM+G Optimising model 19 of 56: SYM+I Optimising model 20 of 56: SYM+I+G Optimising model 21 of 56: GTR Optimising model 22 of 56: GTR+G Optimising model 23 of 56: GTR+I Optimising model 24 of 56: GTR+I+G Optimising model 25 of 56: TrN Optimising model 26 of 56: TrN+G Optimising model 27 of 56: TrN+I Optimising model 28 of 56: TrN+I+G Optimising model 29 of 56: TrNef Optimising model 30 of 56: TrNef+G Optimising model 31 of 56: TrNef+I Optimising model 32 of 56: TrNef+I+G Optimising model 33 of 56: TVM Optimising model 34 of 56: TVM+G Optimising model 35 of 56: TVM+I Optimising model 36 of 56: TVM+I+G Optimising model 37 of 56: TVMef Optimising model 38 of 56: TVMef+G Optimising model 39 of 56: TVMef+I Optimising model 40 of 56: TVMef+I+G Optimising model 41 of 56: TIM Optimising model 42 of 56: TIM+G Optimising model 43 of 56: TIM+I Optimising model 44 of 56: TIM+I+G Optimising model 45 of 56: TIMef Optimising model 46 of 56: TIMef+G Optimising model 47 of 56: TIMef+I Optimising model 48 of 56: TIMef+I+G Optimising model 49 of 56: K81uf Optimising model 50 of 56: K81uf+G Optimising model 51 of 56: K81uf+I Optimising model 52 of 56: K81uf+I+G Optimising model 53 of 56: K81 Optimising model 54 of 56: K81+G Optimising model 55 of 56: K81+I Optimising model 56 of 56: K81+I+G Uniform G I I+G JC -3812.840382188315 -3790.0312102599682 -3789.913205076167 -3790.0933125813117 F81 -3761.9642083881286 -3738.2348056327987 -3738.186801862341 -3738.2802087206865 HKY -3594.576076292913 -3555.2175027297258 -3555.76378725449 -3554.481979839641 K80 -3656.12539434177 -3623.24844182771 -3623.711805796726 -3622.8933323760443 SYM -3629.348467997846 -3598.960772989927 -3598.724733932736 -3597.446836081639 GTR -3575.626546987094 -3542.545266016192 -3542.828082001768 -3540.960762708277 TrN -3582.1826205623206 -3547.6161793255505 -3548.7833014463254 -3546.79520387938 TrNef -3640.841188873327 -3609.910630403013 -3610.7971442435733 -3609.453715410685 TVM -3586.8767518816426 -3550.4701526872345 -3550.6268582993744 -3549.5608267090197 TVMef -3643.1885617465973 -3611.965135620083 -3611.5943873842957 -3611.81308242761 TIM -3582.045086752845 -3547.697419990652 -3548.6773765114044 -3546.69958603607 TIMef -3641.0194129539364 -3610.245175911722 -3610.8345819836513 -3609.5414393588862 K81uf -3594.2994420429736 -3555.1565706513757 -3555.6357523297775 -3554.3431820081883 K81 -3655.9890634398753 -3623.2636582407063 -3623.6736462679655 -3622.9321963253033 ****Hierarchical Likelihood Ratio Tests (hLRTs)**** Equal base frequencies Null model = JC Alternative model = F81 2(lnL1-lnL0) = 101.75234760037256 df = 3 Using Chi-Squared Test P-value < .0001 Ti=Tv Null model = F81 Alternative model = HKY 2(lnL1-lnL0) = 334.776264190431 df = 1 Using Chi-Squared Test P-value < .0001 1 or 2 transition rates Null model = HKY Alternative model = TrN 2(lnL1-lnL0) = 24.7869114611849 df = 1 Using Chi-Squared Test P-value < .0001 1 or 2 transversion rates Null model = TrN Alternative model = TIM 2(lnL1-lnL0) = 0.27506761895165255 df = 1 Using Chi-Squared Test P-value = 0.45826244137645167 Equal rates among sites Null model = TrN Alternative model = TrN+G 2(lnL1-lnL0) = 69.13288247354012 df = 1 Using mixed Chi-Squared Test P-value < .0001 No invariable sites Null model = TrN+G Alternative model = TrN+I+G 2(lnL1-lnL0) = 1.6419508923409012 df = 1 Using mixed Chi-Squared Test P-value = 0.034981210099557236 Model Selected: TrN+G -lnL: 3547.6161793255505 Substitution Model (with Rate Distribution): Model of substitution: TN (Tamura-Nei 1993) Transition/transversion rate ratio kappa: 14.26 Y/R transition rate ratio: 2.19 Nucleotide frequencies: pi(A) = 0.35442 pi(C) = 0.25565 pi(G) = 0.17043 pi(T) = 0.21950 Expected transition/transversion ratio: 6.57 Expected pyrimidine transition/purine transition ratio: 2.03 Model of rate heterogeneity: Discrete Gamma Number of rate categories: 4 Gamma distribution parameter alpha: 0.17 Relative rates and their probabilities: Rate Probability 1 0.00003 0.25000 2 0.01861 0.25000 3 0.38041 0.25000 4 3.60095 0.25000 ****Akaike Information Criterion 1 (AIC1)**** Model Selected: GTR+I+G -lnL = 3540.960762708277 k = 17 (Branch lengths included as model parameters) AIC1 = 7115.921525416554 Substitution Model (with Rate Distribution): Model of substitution: GTR (Lanave et al. 1984) Parameter a: 2.05 Parameter b: 14.67 Parameter c: 2.61 Parameter d: 0.47 Parameter e: 34.07 A C G T Corresponding rate matrix ---------------- (shown without frequencies): A a b c C d e G 1 Nucleotide frequencies: pi(A) = 0.35116 pi(C) = 0.25630 pi(G) = 0.17456 pi(T) = 0.21797 Expected transition/transversion ratio: 6.31 Expected pyrimidine transition/purine transition ratio: 2.12 Model of rate heterogeneity: Discrete Gamma + Invariable sites Number of rate categories: 1 + 4 Gamma distribution parameter alpha: 0.38 Proportion of invariable sites: 0.31 Relative rates and their probabilities: Rate Probability 1 0.00000 0.31339 2 0.01509 0.17165 3 0.27599 0.17165 4 1.19974 0.17165 5 4.33494 0.17165 ****Akaike Information Criterion 2 (AIC2)**** Model Selected: TrN+G -lnL = 3547.6161793255505 k = 13 (Branch lengths included as model parameters) AIC2 = 7160.232358651101 Substitution Model (with Rate Distribution): Model of substitution: TN (Tamura-Nei 1993) Transition/transversion rate ratio kappa: 14.26 Y/R transition rate ratio: 2.19 Nucleotide frequencies: pi(A) = 0.35442 pi(C) = 0.25565 pi(G) = 0.17043 pi(T) = 0.21950 Expected transition/transversion ratio: 6.57 Expected pyrimidine transition/purine transition ratio: 2.03 Model of rate heterogeneity: Discrete Gamma Number of rate categories: 4 Gamma distribution parameter alpha: 0.17 Relative rates and their probabilities: Rate Probability 1 0.00003 0.25000 2 0.01861 0.25000 3 0.38041 0.25000 4 3.60095 0.25000 ****Bayesian Information Criterion (BIC)**** Model Selected: TrN+G -lnL = 3547.6161793255505 k = 13 (Branch lengths included as model parameters) BIC = 7190.830748946296 Substitution Model (with Rate Distribution): Model of substitution: TN (Tamura-Nei 1993) Transition/transversion rate ratio kappa: 14.26 Y/R transition rate ratio: 2.19 Nucleotide frequencies: pi(A) = 0.35442 pi(C) = 0.25565 pi(G) = 0.17043 pi(T) = 0.21950 Expected transition/transversion ratio: 6.57 Expected pyrimidine transition/purine transition ratio: 2.03 Model of rate heterogeneity: Discrete Gamma Number of rate categories: 4 Gamma distribution parameter alpha: 0.17 Relative rates and their probabilities: Rate Probability 1 0.00003 0.25000 2 0.01861 0.25000 3 0.38041 0.25000 4 3.60095 0.25000 Model-fit Ranking according to all measures ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- AIC1 Model Ln AIC2 Model Ln BIC Model Ln ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 0 7115.921525416554 GTR+I+G -3540.960762708277 7160.232358651101 TrN+G -3547.6161793255505 7190.830748946296 TrN+G -3547.6161793255505 1 7117.090532032384 GTR+G -3542.545266016192 7162.566602892651 TrN+I -3548.7833014463254 7193.1649931878455 TrN+I -3548.7833014463254 2 7117.656164003536 GTR+I -3542.828082001768 7163.59040775876 TrN+I+G -3546.79520387938 7196.542520384355 TrN+I+G -3546.79520387938 3 7121.232358651101 TrN+G -3547.6161793255505 7165.090532032384 GTR+G -3542.545266016192 7198.346952606899 TIM+G -3547.697419990652 4 7121.59040775876 TrN+I+G -3546.79520387938 7165.394839981304 TIM+G -3547.697419990652 7198.679673424247 HKY+G -3555.2175027297258 5 7123.394839981304 TIM+G -3547.697419990652 7165.656164003536 GTR+I -3542.828082001768 7199.772242473776 HKY+I -3555.76378725449 6 7123.39917207214 TIM+I+G -3546.69958603607 7166.921525416554 GTR+I+G -3540.960762708277 7200.306865648404 TIM+I -3548.6773765114044 7 7123.566602892651 TrN+I -3548.7833014463254 7167.354753022809 TIM+I -3548.6773765114044 7202.750089318778 GTR+G -3542.545266016192 8 7125.354753022809 TIM+I -3548.6773765114044 7168.39917207214 TIM+I+G -3546.69958603607 7203.3157212899305 GTR+I -3542.828082001768 9 7130.940305374469 TVM+G -3550.4701526872345 7170.4350054594515 HKY+G -3555.2175027297258 7203.705007028134 TIM+I+G -3546.69958603607 10 7131.121653418039 TVM+I+G -3549.5608267090197 7171.52757450898 HKY+I -3555.76378725449 7204.562349974477 HKY+I+G -3554.481979839641 11 7131.253716598749 TVM+I -3550.6268582993744 7173.963959679282 HKY+I+G -3554.481979839641 7205.911531597946 K81uf+G -3555.1565706513757 12 7134.4350054594515 HKY+G -3555.2175027297258 7175.313141302751 K81uf+G -3555.1565706513757 7206.86989495475 K81uf+I -3555.6357523297775 13 7134.963959679282 HKY+I+G -3554.481979839641 7175.940305374469 TVM+G -3550.4701526872345 7206.934805033347 GTR+I+G -3540.960762708277 14 7135.52757450898 HKY+I -3555.76378725449 7176.253716598749 TVM+I -3550.6268582993744 7211.246140330463 TVM+G -3550.4701526872345 15 7136.313141302751 K81uf+G -3555.1565706513757 7176.271504659555 K81uf+I -3555.6357523297775 7211.559551554743 TVM+I -3550.6268582993744 16 7136.6863640163765 K81uf+I+G -3554.3431820081883 7178.6863640163765 K81uf+I+G -3554.3431820081883 7211.6384766419715 K81uf+I+G -3554.3431820081883 17 7137.271504659555 K81uf+I -3555.6357523297775 7179.121653418039 TVM+I+G -3549.5608267090197 7216.781210704434 TVM+I+G -3549.5608267090197 18 7181.253093974188 GTR -3575.626546987094 7224.365241124641 TrN -3582.1826205623206 7252.609909089437 TrN -3582.1826205623206 19 7188.365241124641 TrN -3582.1826205623206 7226.253093974188 GTR -3575.626546987094 7259.688563800884 TIM -3582.045086752845 20 7190.09017350569 TIM -3582.045086752845 7229.09017350569 TIM -3582.045086752845 7261.558928930182 GTR -3575.626546987094 21 7201.753503763285 TVM -3586.8767518816426 7243.753503763285 TVM -3586.8767518816426 7270.043098220222 HKY -3594.576076292913 22 7211.152152585826 HKY -3594.576076292913 7244.152152585826 HKY -3594.576076292913 7276.70561638888 TVM -3586.8767518816426 23 7212.598884085947 K81uf -3594.2994420429736 7248.598884085947 K81uf -3594.2994420429736 7276.843552050743 K81uf -3594.2994420429736 24 7222.893672163278 SYM+I+G -3597.446836081639 7262.449467865472 SYM+I -3598.724733932736 7293.047858160667 SYM+I -3598.724733932736 25 7223.449467865472 SYM+I -3598.724733932736 7262.921545979854 SYM+G -3598.960772989927 7293.358484110022 TrNef+G -3609.910630403013 26 7223.921545979854 SYM+G -3598.960772989927 7264.893672163278 SYM+I+G -3597.446836081639 7293.519936275049 SYM+G -3598.960772989927 27 7239.821260806026 TrNef+G -3609.910630403013 7269.821260806026 TrNef+G -3609.910630403013 7295.131511791143 TrNef+I -3610.7971442435733 28 7240.90743082137 TrNef+I+G -3609.453715410685 7271.5942884871465 TrNef+I -3610.7971442435733 7297.845784788873 SYM+I+G -3597.446836081639 29 7241.5942884871465 TrNef+I -3610.7971442435733 7273.90743082137 TrNef+I+G -3609.453715410685 7299.798376455767 TrNef+I+G -3609.453715410685 30 7242.490351823444 TIMef+G -3610.245175911722 7275.490351823444 TIMef+G -3610.245175911722 7301.38129745784 TIMef+G -3610.245175911722 31 7243.0828787177725 TIMef+I+G -3609.5414393588862 7276.669163967303 TIMef+I -3610.8345819836513 7302.560109601699 TIMef+I -3610.8345819836513 32 7243.669163967303 TIMef+I -3610.8345819836513 7279.0828787177725 TIMef+I+G -3609.5414393588862 7307.327546682568 TIMef+I+G -3609.5414393588862 33 7247.188774768591 TVMef+I -3611.5943873842957 7283.188774768591 TVMef+I -3611.5943873842957 7311.433442733387 TVMef+I -3611.5943873842957 34 7247.930271240166 TVMef+G -3611.965135620083 7283.930271240166 TVMef+G -3611.965135620083 7312.174939204961 TVMef+G -3611.965135620083 35 7249.62616485522 TVMef+I+G -3611.81308242761 7288.62616485522 TVMef+I+G -3611.81308242761 7312.680384629017 K80+G -3623.24844182771 36 7264.49688365542 K80+G -3623.24844182771 7291.49688365542 K80+G -3623.24844182771 7313.607112567049 K80+I -3623.711805796726 37 7265.423611593452 K80+I -3623.711805796726 7292.423611593452 K80+I -3623.711805796726 7319.224555150415 TVMef+I+G -3611.81308242761 38 7265.786664752089 K80+I+G -3622.8933323760443 7295.786664752089 K80+I+G -3622.8933323760443 7319.323888056085 K80+I+G -3622.8933323760443 39 7266.5273164814125 K81+G -3623.2636582407063 7296.5273164814125 K81+G -3623.2636582407063 7320.064539785409 K81+G -3623.2636582407063 40 7267.347292535931 K81+I -3623.6736462679655 7297.347292535931 K81+I -3623.6736462679655 7320.884515839927 K81+I -3623.6736462679655 41 7267.8643926506065 K81+I+G -3622.9321963253033 7300.8643926506065 K81+I+G -3622.9321963253033 7326.755338285003 K81+I+G -3622.9321963253033 42 7282.696935995692 SYM -3629.348467997846 7318.696935995692 SYM -3629.348467997846 7346.941603960488 SYM -3629.348467997846 43 7299.682377746654 TrNef -3640.841188873327 7326.682377746654 TrNef -3640.841188873327 7347.865878720251 TrNef -3640.841188873327 44 7302.038825907873 TIMef -3641.0194129539364 7332.038825907873 TIMef -3641.0194129539364 7355.576049211869 TIMef -3641.0194129539364 45 7308.377123493195 TVMef -3643.1885617465973 7341.377123493195 TVMef -3643.1885617465973 7367.268069127591 TVMef -3643.1885617465973 46 7328.25078868354 K80 -3656.12539434177 7352.25078868354 K80 -3656.12539434177 7371.080567326737 K80 -3656.12539434177 47 7329.978126879751 K81 -3655.9890634398753 7356.978126879751 K81 -3655.9890634398753 7378.161627853347 K81 -3655.9890634398753 48 7498.373603724682 F81+I -3738.186801862341 7531.373603724682 F81+I -3738.186801862341 7557.264549359078 F81+I -3738.186801862341 49 7498.469611265597 F81+G -3738.2348056327987 7531.469611265597 F81+G -3738.2348056327987 7557.360556899994 F81+G -3738.2348056327987 50 7500.560417441373 F81+I+G -3738.2802087206865 7536.560417441373 F81+I+G -3738.2802087206865 7564.8050854061685 F81+I+G -3738.2802087206865 51 7543.928416776257 F81 -3761.9642083881286 7573.928416776257 F81 -3761.9642083881286 7597.465640080253 F81 -3761.9642083881286 52 7595.826410152334 JC+I -3789.913205076167 7619.826410152334 JC+I -3789.913205076167 7638.65618879553 JC+I -3789.913205076167 53 7596.0624205199365 JC+G -3790.0312102599682 7620.0624205199365 JC+G -3790.0312102599682 7638.892199163133 JC+G -3790.0312102599682 54 7598.186625162623 JC+I+G -3790.0933125813117 7625.186625162623 JC+I+G -3790.0933125813117 7646.37012613622 JC+I+G -3790.0933125813117 55 7639.68076437663 JC -3812.840382188315 7660.68076437663 JC -3812.840382188315 7677.156820689427 JC -3812.840382188315 56 7639.68076437663 JC -3812.840382188315 7660.68076437663 JC -3812.840382188315 7677.156820689427 JC -3812.840382188315 Analysis took: 0 minutes 9 seconds