--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 03 11:19:58 WET 2017 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=CLUSTALW2 tcoffee.params= tcoffee.maxSeqs=0 codeml.bin=codeml mrbayes.tburnin=2500 codeml.dir= input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb_adops tcoffee.bin=t_coffee_ADOPS mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta= input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/Srevisao1/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) (Values are saved to the file /opt/ADOPS1/Srevisao1/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -7545.50 -7563.99 2 -7544.86 -7568.18 -------------------------------------- TOTAL -7545.13 -7567.51 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/Srevisao1/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": Summaries are based on a total of 3002 samples from 2 runs. Each run produced 2001 samples of which 1501 samples were included. Parameter summaries saved to file "/opt/ADOPS1/Srevisao1/S5_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.469208 0.003508 1.350087 1.578394 1.468084 1498.65 1499.82 1.000 r(A<->C){all} 0.107501 0.000134 0.084432 0.129230 0.106798 1008.14 1015.87 1.000 r(A<->G){all} 0.320348 0.000335 0.284494 0.356604 0.319870 903.62 940.71 1.001 r(A<->T){all} 0.083122 0.000065 0.068407 0.099767 0.082883 1081.42 1179.92 1.000 r(C<->G){all} 0.143599 0.000213 0.115425 0.172392 0.143039 1013.84 1015.05 1.000 r(C<->T){all} 0.262472 0.000285 0.228995 0.294284 0.262325 772.45 914.42 1.000 r(G<->T){all} 0.082959 0.000082 0.066133 0.102474 0.082508 960.09 971.38 1.000 pi(A){all} 0.292989 0.000114 0.272272 0.313511 0.292875 947.09 982.35 1.001 pi(C){all} 0.174676 0.000076 0.158774 0.192560 0.174447 1044.93 1074.65 1.000 pi(G){all} 0.193692 0.000082 0.175236 0.210526 0.193632 785.24 825.35 1.000 pi(T){all} 0.338643 0.000135 0.315395 0.360700 0.338227 840.18 941.82 1.002 alpha{1,2} 1.007668 0.037610 0.685566 1.371147 0.978509 1063.82 1103.30 1.000 alpha{3} 1.525199 0.159300 0.912001 2.316682 1.448358 1127.18 1285.60 1.000 pinvar{all} 0.060690 0.001948 0.000012 0.146064 0.051403 1026.57 1096.92 1.000 ------------------------------------------------------------------------------------------------------ * Convergence diagnostic (ESS = Estimated Sample Size); min and avg values correspond to minimal and average ESS among runs. ESS value below 100 may indicate that the parameter is undersampled. + Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman and Rubin, 1992) should approach 1.0 as runs converge. Setting sumt conformat to Simple --- CODEML SUMMARY Model 1: NearlyNeutral -3660.050783 Model 2: PositiveSelection -3636.130604 Model 0: one-ratio -3740.088089 Model 3: discrete -3633.973648 Model 7: beta -3659.557345 Model 8: beta&w>1 -3633.174241 Model 0 vs 1 160.07461199999943 Model 2 vs 1 47.84035800000038 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S5_SFBB1) Pr(w>1) post mean +- SE for w 8 L 0.560 2.662 35 R 0.872 3.590 43 I 0.999** 3.967 45 T 0.999** 3.968 62 Q 0.830 3.464 74 Q 0.542 2.611 77 Y 0.677 3.011 106 E 0.997** 3.962 109 C 0.952* 3.827 125 T 1.000** 3.970 127 E 0.964* 3.864 155 K 0.683 3.028 175 P 0.734 3.180 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S5_SFBB1) Pr(w>1) post mean +- SE for w 35 R 0.823 3.567 +- 1.326 43 I 0.999** 4.175 +- 0.691 45 T 0.999** 4.177 +- 0.687 62 Q 0.793 3.497 +- 1.404 77 Y 0.602 2.824 +- 1.558 106 E 0.996** 4.167 +- 0.707 109 C 0.936 3.966 +- 1.010 125 T 1.000** 4.179 +- 0.683 127 E 0.953* 4.023 +- 0.940 155 K 0.606 2.841 +- 1.559 175 P 0.674 3.084 +- 1.541 Model 8 vs 7 52.766208000000006 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S5_SFBB1) Pr(w>1) post mean +- SE for w 8 L 0.706 2.673 20 G 0.589 2.374 35 R 0.917 3.197 43 I 0.999** 3.401 45 T 0.999** 3.402 62 Q 0.878 3.097 74 Q 0.666 2.566 77 Y 0.794 2.892 106 E 0.997** 3.396 109 C 0.968* 3.324 125 T 1.000** 3.403 127 E 0.975* 3.342 155 K 0.792 2.886 175 P 0.829 2.976 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S5_SFBB1) Pr(w>1) post mean +- SE for w 8 L 0.621 2.390 +- 1.262 20 G 0.519 2.114 +- 1.268 35 R 0.879 3.145 +- 1.036 43 I 0.999** 3.499 +- 0.680 45 T 0.999** 3.500 +- 0.678 62 Q 0.845 3.064 +- 1.120 74 Q 0.600 2.354 +- 1.303 77 Y 0.721 2.680 +- 1.229 106 E 0.997** 3.492 +- 0.690 109 C 0.958* 3.381 +- 0.840 125 T 1.000** 3.501 +- 0.676 127 E 0.968* 3.411 +- 0.806 155 K 0.719 2.677 +- 1.239 175 P 0.775 2.851 +- 1.206