--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Sep 29 05:24:47 WEST 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=/opt/ADOPS1/ASP1/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/ASP1/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/ASP1/ClustalW2/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/ASP1/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -11375.06 -11433.98 2 -11374.67 -11436.60 -------------------------------------- TOTAL -11374.84 -11435.98 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/ASP1/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/ASP1/ClustalW2/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/ASP1/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 15.989573 0.778511 14.342760 17.763120 15.982220 644.77 710.78 1.000 r(A<->C){all} 0.065064 0.000079 0.047897 0.081700 0.064687 247.02 347.70 1.000 r(A<->G){all} 0.288662 0.000528 0.247687 0.339218 0.287788 122.14 148.37 1.000 r(A<->T){all} 0.079213 0.000072 0.062098 0.095351 0.078794 198.38 345.14 1.000 r(C<->G){all} 0.069071 0.000103 0.050607 0.089123 0.068486 338.57 423.25 1.001 r(C<->T){all} 0.320775 0.000556 0.272428 0.365624 0.320839 104.38 130.91 1.000 r(G<->T){all} 0.177214 0.000212 0.149051 0.205834 0.176951 353.13 365.46 1.000 pi(A){all} 0.217401 0.000162 0.191721 0.241587 0.217229 248.91 261.42 1.000 pi(C){all} 0.264986 0.000123 0.243987 0.287186 0.265164 210.22 278.47 1.000 pi(G){all} 0.158398 0.000125 0.136733 0.179248 0.158176 124.32 168.58 1.000 pi(T){all} 0.359215 0.000180 0.333236 0.385040 0.358817 195.03 212.64 1.000 alpha{1,2} 0.544395 0.001351 0.474182 0.617942 0.544140 881.23 1035.37 1.000 alpha{3} 0.669775 0.002347 0.569779 0.761964 0.668596 688.51 858.56 1.001 pinvar{all} 0.338157 0.000551 0.290867 0.381309 0.338230 802.41 965.66 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 -6337.020012 Model 2: PositiveSelection -6228.794468 Model 0: one-ratio -6683.0048 Model 3: discrete -6226.583334 Model 7: beta -6333.602326 Model 8: beta&w>1 -6221.989614 Model 0 vs 1 691.9695759999995 Model 2 vs 1 216.4510879999998 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 01_AE.AF.07.569M.GQ477441) Pr(w>1) post mean +- SE for w 9 I 1.000** 4.356 103 S 0.999** 4.353 107 P 1.000** 4.356 119 T 1.000** 4.356 120 Q 0.998** 4.349 123 I 1.000** 4.356 125 L 0.999** 4.354 135 A 1.000** 4.356 151 S 0.827 3.777 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: 01_AE.AF.07.569M.GQ477441) Pr(w>1) post mean +- SE for w 9 I 1.000** 4.499 +- 0.233 103 S 0.999** 4.494 +- 0.268 107 P 1.000** 4.499 +- 0.233 119 T 1.000** 4.499 +- 0.233 120 Q 0.998** 4.491 +- 0.291 123 I 1.000** 4.499 +- 0.233 125 L 0.999** 4.497 +- 0.251 135 A 0.999** 4.497 +- 0.246 151 S 0.757 3.625 +- 1.497 Model 8 vs 7 223.2254240000002 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 01_AE.AF.07.569M.GQ477441) Pr(w>1) post mean +- SE for w 9 I 1.000** 3.920 103 S 1.000** 3.919 107 P 1.000** 3.920 119 T 1.000** 3.920 120 Q 0.999** 3.917 123 I 1.000** 3.920 125 L 1.000** 3.918 135 A 1.000** 3.919 141 I 0.548 2.550 151 S 0.950* 3.769 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: 01_AE.AF.07.569M.GQ477441) Pr(w>1) post mean +- SE for w 9 I 1.000** 4.097 +- 0.494 103 S 0.999** 4.092 +- 0.508 107 P 1.000** 4.097 +- 0.494 119 T 1.000** 4.097 +- 0.494 120 Q 0.998** 4.089 +- 0.518 123 I 1.000** 4.097 +- 0.494 125 L 0.999** 4.094 +- 0.502 135 A 0.999** 4.095 +- 0.500 151 S 0.688 2.997 +- 1.446