--- 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
