--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Nov 04 02:14:22 WET 2017 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=MUSCLE 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/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S9/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/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -8659.11 -8678.27 2 -8660.05 -8685.87 -------------------------------------- TOTAL -8659.47 -8685.18 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S9/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/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.558293 0.003613 1.446847 1.677442 1.556226 1416.88 1458.94 1.000 r(A<->C){all} 0.107070 0.000111 0.087674 0.128343 0.106703 832.61 970.19 1.000 r(A<->G){all} 0.296124 0.000334 0.260845 0.332910 0.295945 595.85 769.66 1.000 r(A<->T){all} 0.075597 0.000052 0.061279 0.088632 0.075333 1160.76 1161.35 1.001 r(C<->G){all} 0.168509 0.000213 0.138106 0.195547 0.168272 745.59 938.09 1.000 r(C<->T){all} 0.278580 0.000299 0.245780 0.311627 0.278315 831.29 879.13 1.000 r(G<->T){all} 0.074119 0.000066 0.058141 0.089658 0.073852 973.41 1124.51 1.000 pi(A){all} 0.303728 0.000123 0.283066 0.325835 0.303460 906.22 929.80 1.000 pi(C){all} 0.169499 0.000071 0.153626 0.186668 0.169281 1059.32 1085.98 1.001 pi(G){all} 0.186026 0.000080 0.168376 0.202547 0.185892 766.40 883.99 1.000 pi(T){all} 0.340747 0.000136 0.318077 0.363741 0.340559 892.74 897.73 1.001 alpha{1,2} 0.850847 0.012325 0.651088 1.081700 0.838039 1051.10 1236.90 1.000 alpha{3} 1.624522 0.108844 1.092232 2.319610 1.580005 1306.98 1316.63 1.000 pinvar{all} 0.033997 0.000743 0.000004 0.088343 0.027645 1295.71 1299.51 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 -5488.987427 Model 2: PositiveSelection -5451.403633 Model 0: one-ratio -5622.903996 Model 3: discrete -5449.402515 Model 7: beta -5495.653586 Model 8: beta&w>1 -5451.373108 Model 0 vs 1 267.83313799999996 Model 2 vs 1 75.16758800000025 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S3_S9_AB539854_MdFBX11) Pr(w>1) post mean +- SE for w 14 T 0.986* 3.484 20 N 1.000** 3.519 24 Q 0.989* 3.491 53 L 0.955* 3.407 58 Y 0.724 2.823 60 L 0.991** 3.498 62 L 0.784 2.975 73 A 0.729 2.836 99 K 0.970* 3.443 107 V 0.999** 3.517 109 R 1.000** 3.518 138 R 0.597 2.505 155 T 0.785 2.977 170 K 0.964* 3.430 173 S 0.784 2.974 189 T 1.000** 3.519 191 A 0.978* 3.464 219 K 0.757 2.908 242 E 0.511 2.287 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: S3_S9_AB539854_MdFBX11) Pr(w>1) post mean +- SE for w 14 T 0.980* 3.555 +- 0.485 20 N 1.000** 3.608 +- 0.330 24 Q 0.985* 3.569 +- 0.453 53 L 0.940 3.450 +- 0.692 58 Y 0.653 2.677 +- 1.243 60 L 0.989* 3.581 +- 0.422 62 L 0.728 2.885 +- 1.180 73 A 0.661 2.702 +- 1.240 99 K 0.960* 3.502 +- 0.603 107 V 0.999** 3.606 +- 0.337 109 R 0.999** 3.607 +- 0.332 138 R 0.529 2.361 +- 1.303 155 T 0.730 2.891 +- 1.179 170 K 0.951* 3.478 +- 0.643 173 S 0.728 2.884 +- 1.180 189 T 1.000** 3.609 +- 0.327 191 A 0.971* 3.533 +- 0.541 219 K 0.695 2.793 +- 1.213 Model 8 vs 7 88.56095600000117 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S3_S9_AB539854_MdFBX11) Pr(w>1) post mean +- SE for w 14 T 0.994** 2.991 20 N 1.000** 3.003 24 Q 0.995** 2.992 53 L 0.979* 2.960 58 Y 0.876 2.742 60 L 0.995** 2.993 62 L 0.893 2.777 72 T 0.533 2.003 73 A 0.872 2.731 85 R 0.589 2.113 99 K 0.986* 2.973 107 V 1.000** 3.002 109 R 1.000** 3.003 126 Q 0.658 2.267 138 R 0.762 2.493 141 Y 0.635 2.229 155 T 0.890 2.769 170 K 0.985* 2.972 173 S 0.898 2.787 189 T 1.000** 3.003 191 A 0.990* 2.981 214 R 0.621 2.193 219 K 0.881 2.751 239 R 0.639 2.228 242 E 0.734 2.438 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: S3_S9_AB539854_MdFBX11) Pr(w>1) post mean +- SE for w 14 T 0.993** 2.771 +- 0.481 20 N 1.000** 2.786 +- 0.460 24 Q 0.994** 2.773 +- 0.480 53 L 0.977* 2.736 +- 0.530 58 Y 0.874 2.492 +- 0.722 60 L 0.995** 2.775 +- 0.478 62 L 0.893 2.544 +- 0.708 72 T 0.629 1.966 +- 0.893 73 A 0.871 2.491 +- 0.735 85 R 0.651 2.022 +- 0.923 99 K 0.985* 2.752 +- 0.509 107 V 0.999** 2.785 +- 0.462 109 R 1.000** 2.785 +- 0.461 126 Q 0.705 2.132 +- 0.893 138 R 0.784 2.304 +- 0.843 141 Y 0.704 2.119 +- 0.855 155 T 0.890 2.539 +- 0.717 170 K 0.983* 2.748 +- 0.512 173 S 0.897 2.553 +- 0.700 189 T 1.000** 2.786 +- 0.460 191 A 0.989* 2.762 +- 0.496 214 R 0.686 2.082 +- 0.875 219 K 0.880 2.512 +- 0.724 239 R 0.693 2.105 +- 0.892 242 E 0.764 2.248 +- 0.833