--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Feb 15 07:45:40 WET 2016 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=/usr/bin/ input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb tcoffee.bin=t_coffee mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_2/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_2/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/ADOPS/DATA/Zika/B4_A/Zika-NS5_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -9304.41 -9381.82 2 -9291.47 -9390.41 -------------------------------------- TOTAL -9292.16 -9389.72 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_2/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/ADOPS/DATA/Zika/B4_A/Zika-NS5_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.113870 0.003214 1.009052 1.225373 1.111789 390.79 719.74 1.001 r(A<->C){all} 0.021185 0.000017 0.013530 0.029356 0.020941 488.45 617.70 1.000 r(A<->G){all} 0.227548 0.000480 0.188769 0.272857 0.227187 342.30 344.73 1.003 r(A<->T){all} 0.026057 0.000029 0.016242 0.036799 0.025678 648.91 750.34 1.000 r(C<->G){all} 0.003915 0.000004 0.000852 0.007819 0.003620 874.00 926.66 1.001 r(C<->T){all} 0.700352 0.000597 0.652946 0.747404 0.700571 308.24 325.42 1.004 r(G<->T){all} 0.020942 0.000021 0.012679 0.030081 0.020502 663.61 665.81 1.001 pi(A){all} 0.279547 0.000061 0.265343 0.296039 0.279324 822.39 943.99 1.000 pi(C){all} 0.229257 0.000051 0.215084 0.242748 0.229051 930.41 935.39 1.000 pi(G){all} 0.296180 0.000068 0.279129 0.311338 0.296114 784.05 934.16 1.000 pi(T){all} 0.195016 0.000046 0.181966 0.208017 0.194854 877.53 909.85 1.000 alpha{1,2} 0.115638 0.000077 0.099209 0.133175 0.115643 713.06 848.31 1.002 alpha{3} 4.900763 1.057870 2.992786 6.838979 4.792453 1121.42 1238.76 1.000 pinvar{all} 0.304543 0.000735 0.249271 0.353512 0.305057 693.11 758.37 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 -8858.089584 Model 2: PositiveSelection -8839.577705 Model 0: one-ratio -8951.168691 Model 3: discrete -8837.678915 Model 7: beta -8863.904788 Model 8: beta&w>1 -8839.004753 Model 0 vs 1 186.15821400000277 Model 2 vs 1 37.02375799999936 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: gb:KX766029|Organism:Zika virus|Strain Name:R116265|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5) Pr(w>1) post mean +- SE for w 522 R 1.000** 18.221 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: gb:KX766029|Organism:Zika virus|Strain Name:R116265|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5) Pr(w>1) post mean +- SE for w 73 Y 0.752 2.909 +- 2.506 200 Y 0.550 1.967 +- 1.651 522 R 0.996** 3.822 +- 2.928 636 S 0.710 2.671 +- 2.323 Model 8 vs 7 49.80007000000114 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: gb:KX766029|Organism:Zika virus|Strain Name:R116265|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5) Pr(w>1) post mean +- SE for w 522 R 1.000** 17.873 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: gb:KX766029|Organism:Zika virus|Strain Name:R116265|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5) Pr(w>1) post mean +- SE for w 73 Y 0.943 1.546 +- 0.435 138 P 0.543 1.031 +- 0.644 200 Y 0.858 1.452 +- 0.499 227 T 0.845 1.434 +- 0.467 265 V 0.655 1.200 +- 0.562 278 N 0.697 1.256 +- 0.511 320 I 0.795 1.371 +- 0.473 522 R 1.000** 1.598 +- 0.381 523 T 0.522 1.034 +- 0.569 570 Q 0.623 1.142 +- 0.643 636 S 0.937 1.540 +- 0.438 708 H 0.570 1.068 +- 0.642 820 P 0.598 1.107 +- 0.644