--- 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
