--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Tue Oct 31 19:06:37 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/Srevisao/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S24_17Malus/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/Srevisao/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -7321.50 -7347.97 2 -7321.58 -7340.17 -------------------------------------- TOTAL -7321.54 -7347.27 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/Srevisao/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S24_17Malus/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/Srevisao/S24_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.539856 0.004179 1.413577 1.663098 1.538003 1419.39 1460.20 1.000 r(A<->C){all} 0.119535 0.000141 0.097054 0.143637 0.119242 1036.91 1047.19 1.001 r(A<->G){all} 0.302546 0.000355 0.266413 0.340469 0.302185 770.41 852.92 1.000 r(A<->T){all} 0.075273 0.000059 0.061165 0.091108 0.075001 1197.11 1231.75 1.000 r(C<->G){all} 0.155096 0.000238 0.126628 0.185870 0.154708 1011.64 1044.12 1.000 r(C<->T){all} 0.262896 0.000306 0.227563 0.296297 0.262884 813.12 848.51 1.001 r(G<->T){all} 0.084654 0.000086 0.067474 0.102968 0.084501 934.48 1038.18 1.000 pi(A){all} 0.292303 0.000120 0.272481 0.314436 0.292226 971.69 1114.86 1.000 pi(C){all} 0.175291 0.000076 0.159866 0.194298 0.175144 929.34 1002.94 1.000 pi(G){all} 0.196941 0.000092 0.178868 0.214956 0.196643 805.02 926.84 1.000 pi(T){all} 0.335465 0.000130 0.314464 0.358724 0.335305 1106.01 1117.18 1.000 alpha{1,2} 0.731149 0.010507 0.548909 0.935565 0.717856 1218.11 1271.50 1.000 alpha{3} 2.301397 0.358154 1.293062 3.384344 2.209746 1371.55 1419.94 1.000 pinvar{all} 0.043361 0.001042 0.000004 0.103679 0.036569 1229.64 1296.22 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 -3432.591325 Model 2: PositiveSelection -3412.089337 Model 0: one-ratio -3512.847386 Model 3: discrete -3412.070558 Model 7: beta -3436.013498 Model 8: beta&w>1 -3412.652165 Model 0 vs 1 160.5121220000001 Model 2 vs 1 41.003975999999966 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S24_SFBB1) Pr(w>1) post mean +- SE for w 2 E 0.911 3.792 43 R 0.631 2.932 50 I 0.999** 4.060 52 T 0.999** 4.061 69 Q 0.609 2.864 84 Y 0.505 2.548 113 E 0.967* 3.963 116 C 0.961* 3.943 132 T 1.000** 4.062 134 E 0.891 3.728 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: S24_SFBB1) Pr(w>1) post mean +- SE for w 2 E 0.892 3.922 +- 1.238 43 R 0.548 2.687 +- 1.606 50 I 0.999** 4.280 +- 0.764 52 T 0.999** 4.282 +- 0.761 69 Q 0.557 2.774 +- 1.667 113 E 0.946 4.083 +- 1.025 116 C 0.949 4.112 +- 1.025 132 T 1.000** 4.283 +- 0.760 134 E 0.848 3.739 +- 1.337 Model 8 vs 7 46.72266599999966 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S24_SFBB1) Pr(w>1) post mean +- SE for w 2 E 0.943 3.406 43 R 0.791 3.006 50 I 0.999** 3.554 52 T 1.000** 3.555 69 Q 0.729 2.837 81 Q 0.509 2.246 84 Y 0.710 2.794 113 E 0.984* 3.513 116 C 0.976* 3.493 132 T 1.000** 3.555 134 E 0.940 3.398 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: S24_SFBB1) Pr(w>1) post mean +- SE for w 2 E 0.929 3.536 +- 1.022 43 R 0.699 2.789 +- 1.364 50 I 0.999** 3.746 +- 0.743 52 T 1.000** 3.746 +- 0.742 69 Q 0.668 2.735 +- 1.434 84 Y 0.607 2.503 +- 1.387 113 E 0.974* 3.663 +- 0.852 116 C 0.969* 3.655 +- 0.878 132 T 1.000** 3.746 +- 0.741 134 E 0.913 3.474 +- 1.057