--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Tue Oct 31 18:21:44 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/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S1_18Malus/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/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -8479.63 -8499.87 2 -8479.36 -8500.26 -------------------------------------- TOTAL -8479.49 -8500.09 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/Srevisao/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S1_18Malus/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/S1_18Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.641477 0.003773 1.523864 1.763089 1.641311 1382.34 1420.51 1.000 r(A<->C){all} 0.116718 0.000121 0.095979 0.139254 0.116461 981.89 1004.16 1.000 r(A<->G){all} 0.297573 0.000314 0.263542 0.331833 0.297515 785.28 887.87 1.001 r(A<->T){all} 0.072904 0.000055 0.058607 0.086703 0.072651 610.02 882.05 1.000 r(C<->G){all} 0.150503 0.000200 0.123780 0.178502 0.149947 881.76 1014.54 1.000 r(C<->T){all} 0.269613 0.000289 0.239373 0.305731 0.268894 782.75 783.82 1.000 r(G<->T){all} 0.092690 0.000078 0.075987 0.110160 0.092362 1005.27 1154.30 1.000 pi(A){all} 0.296435 0.000116 0.274981 0.317367 0.296339 775.83 909.17 1.000 pi(C){all} 0.170889 0.000073 0.153653 0.186329 0.170796 833.37 941.37 1.000 pi(G){all} 0.189965 0.000079 0.171588 0.206267 0.189872 873.65 985.30 1.000 pi(T){all} 0.342710 0.000129 0.320284 0.364795 0.342453 1100.35 1136.58 1.000 alpha{1,2} 0.844618 0.010717 0.670832 1.059716 0.833556 1244.18 1295.08 1.000 alpha{3} 1.934298 0.163856 1.236261 2.732345 1.886747 1258.27 1339.81 1.000 pinvar{all} 0.026634 0.000518 0.000008 0.072645 0.020524 1257.74 1292.78 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 -6252.628628 Model 2: PositiveSelection -6216.667031 Model 0: one-ratio -6385.849692 Model 3: discrete -6215.149793 Model 7: beta -6260.066885 Model 8: beta&w>1 -6214.282808 Model 0 vs 1 266.4421279999988 Model 2 vs 1 71.92319400000088 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S1_SFBB1) Pr(w>1) post mean +- SE for w 40 N 1.000** 3.403 46 R 1.000** 3.403 50 P 0.996** 3.395 79 L 0.999** 3.401 84 F 0.861 3.069 86 E 0.986* 3.370 88 G 0.760 2.826 98 L 0.527 2.266 99 A 0.891 3.142 125 R 0.514 2.235 132 I 0.966* 3.322 134 T 0.999** 3.400 151 Q 0.884 3.125 162 E 0.536 2.289 195 E 0.601 2.445 214 T 0.996** 3.395 216 E 0.944 3.268 244 K 0.939 3.257 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: S1_SFBB1) Pr(w>1) post mean +- SE for w 40 N 1.000** 3.531 +- 0.260 46 R 1.000** 3.531 +- 0.262 50 P 0.996** 3.522 +- 0.300 79 L 0.999** 3.529 +- 0.268 84 F 0.839 3.113 +- 0.954 86 E 0.986* 3.495 +- 0.395 88 G 0.728 2.830 +- 1.137 99 A 0.876 3.210 +- 0.865 132 I 0.963* 3.438 +- 0.538 134 T 0.999** 3.528 +- 0.276 151 Q 0.876 3.216 +- 0.866 195 E 0.555 2.386 +- 1.252 214 T 0.996** 3.522 +- 0.300 216 E 0.938 3.371 +- 0.660 244 K 0.930 3.351 +- 0.688 Model 8 vs 7 91.5681540000005 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S1_SFBB1) Pr(w>1) post mean +- SE for w 2 R 0.593 2.063 23 M 0.530 1.936 40 N 1.000** 2.918 46 R 1.000** 2.918 50 P 0.999** 2.916 79 L 1.000** 2.918 84 F 0.956* 2.829 86 E 0.994** 2.906 88 G 0.912 2.738 98 L 0.783 2.472 99 A 0.963* 2.844 110 G 0.590 2.055 125 R 0.766 2.436 132 I 0.988* 2.893 134 T 0.999** 2.917 151 Q 0.949 2.813 162 E 0.792 2.491 163 Q 0.526 1.918 166 Y 0.607 2.112 180 T 0.532 1.935 195 E 0.842 2.595 198 C 0.639 2.169 214 T 0.998** 2.915 216 E 0.980* 2.877 244 K 0.980* 2.878 267 T 0.691 2.282 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: S1_SFBB1) Pr(w>1) post mean +- SE for w 2 R 0.626 1.980 +- 0.953 23 M 0.584 1.883 +- 0.934 40 N 1.000** 2.841 +- 0.482 46 R 1.000** 2.840 +- 0.482 50 P 0.999** 2.838 +- 0.486 79 L 1.000** 2.840 +- 0.483 84 F 0.943 2.704 +- 0.637 86 E 0.994** 2.827 +- 0.504 88 G 0.894 2.587 +- 0.731 98 L 0.769 2.291 +- 0.864 99 A 0.956* 2.736 +- 0.611 110 G 0.623 1.968 +- 0.950 125 R 0.756 2.262 +- 0.875 132 I 0.987* 2.810 +- 0.527 134 T 0.999** 2.840 +- 0.484 151 Q 0.946 2.719 +- 0.639 162 E 0.776 2.305 +- 0.859 163 Q 0.576 1.876 +- 0.966 166 Y 0.643 2.002 +- 0.888 180 T 0.582 1.881 +- 0.947 195 E 0.816 2.397 +- 0.821 198 C 0.662 2.051 +- 0.915 214 T 0.998** 2.837 +- 0.487 216 E 0.977* 2.787 +- 0.556 244 K 0.976* 2.784 +- 0.558 267 T 0.694 2.113 +- 0.889