--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Oct 29 09:29:11 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=/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/Ebola_B1_2/sGP/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/Ebola_B1_2/sGP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1_2/sGP/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/Ebola_B1_2/sGP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -8330.76 -8402.91 2 -8335.96 -8407.55 -------------------------------------- TOTAL -8331.44 -8406.87 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/Ebola_B1_2/sGP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1_2/sGP/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/Ebola_B1_2/sGP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 8.608120 0.460246 7.304150 9.926875 8.570832 158.23 162.82 1.002 r(A<->C){all} 0.191407 0.000227 0.161666 0.219819 0.191166 876.71 903.04 1.000 r(A<->G){all} 0.296941 0.000381 0.258049 0.334413 0.296476 615.83 640.61 1.000 r(A<->T){all} 0.075491 0.000137 0.054840 0.099915 0.075126 737.18 749.74 1.003 r(C<->G){all} 0.047902 0.000123 0.027477 0.070417 0.047465 774.08 785.13 1.000 r(C<->T){all} 0.318411 0.000406 0.278657 0.358112 0.317780 548.45 605.29 1.000 r(G<->T){all} 0.069848 0.000127 0.047812 0.091086 0.069591 737.77 826.14 1.000 pi(A){all} 0.293577 0.000070 0.277855 0.310461 0.293453 926.39 928.09 1.000 pi(C){all} 0.260663 0.000064 0.244192 0.275796 0.260707 775.20 828.39 1.000 pi(G){all} 0.216660 0.000065 0.201384 0.232163 0.216787 521.63 663.18 1.000 pi(T){all} 0.229100 0.000067 0.213663 0.244731 0.229107 813.98 855.69 1.000 alpha{1,2} 0.565982 0.002023 0.476844 0.649458 0.564702 737.79 794.21 1.001 alpha{3} 4.596379 0.955027 2.806196 6.528917 4.471579 814.50 1087.29 1.001 pinvar{all} 0.008384 0.000048 0.000001 0.021935 0.006692 871.69 971.60 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 -5549.145913 Model 2: PositiveSelection -5501.516922 Model 0: one-ratio -5624.826672 Model 3: discrete -5485.762566 Model 7: beta -5566.323159 Model 8: beta&w>1 -5497.630372 Model 0 vs 1 151.3615179999997 Model 2 vs 1 95.257982000001 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:KF827427|Organism:Zaire ebolavirus|Strain Name:rec/COD/1976/Mayinga-rgEBOV|Protein Name:sGP|Gene Symbol:GP) Pr(w>1) post mean +- SE for w 276 T 1.000** 26.512 277 S 1.000** 26.512 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:KF827427|Organism:Zaire ebolavirus|Strain Name:rec/COD/1976/Mayinga-rgEBOV|Protein Name:sGP|Gene Symbol:GP) Pr(w>1) post mean +- SE for w 276 T 1.000** 10.303 +- 0.461 277 S 1.000** 10.303 +- 0.461 Model 8 vs 7 137.3855739999999 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:KF827427|Organism:Zaire ebolavirus|Strain Name:rec/COD/1976/Mayinga-rgEBOV|Protein Name:sGP|Gene Symbol:GP) Pr(w>1) post mean +- SE for w 276 T 1.000** 22.605 277 S 1.000** 22.605 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:KF827427|Organism:Zaire ebolavirus|Strain Name:rec/COD/1976/Mayinga-rgEBOV|Protein Name:sGP|Gene Symbol:GP) Pr(w>1) post mean +- SE for w 276 T 1.000** 10.280 +- 0.488 277 S 1.000** 10.280 +- 0.488