--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Oct 28 20:59:37 WEST 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=
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/Zika-NS5/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Zika-NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Zika-NS5/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/ADOPS1/Zika-NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8973.35         -9074.81
2      -8979.25         -9068.33
--------------------------------------
TOTAL    -8974.04         -9074.12
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Zika-NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Zika-NS5/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/ADOPS1/Zika-NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.026702    0.003294    0.914876    1.137509    1.025019    343.20    521.19    1.001
r(A<->C){all}   0.022490    0.000020    0.014138    0.031228    0.022217    438.11    509.46    1.001
r(A<->G){all}   0.211279    0.000468    0.168389    0.252545    0.209929    297.53    337.46    1.002
r(A<->T){all}   0.023549    0.000028    0.014567    0.034567    0.023168    355.44    513.58    1.000
r(C<->G){all}   0.008323    0.000007    0.003509    0.013474    0.008105    836.30    839.21    1.000
r(C<->T){all}   0.714792    0.000611    0.668123    0.764104    0.715825    273.63    325.48    1.002
r(G<->T){all}   0.019567    0.000021    0.010758    0.028433    0.019167    695.68    731.57    1.000
pi(A){all}      0.279748    0.000067    0.264054    0.295969    0.279753    687.16    917.67    1.000
pi(C){all}      0.228624    0.000053    0.214348    0.242190    0.228614    563.44    771.09    1.000
pi(G){all}      0.295676    0.000068    0.279984    0.311741    0.295834    803.72    892.44    1.000
pi(T){all}      0.195952    0.000049    0.181940    0.209339    0.195731    826.73    931.07    1.000
alpha{1,2}      0.124542    0.000093    0.103971    0.142356    0.124305    875.89   1018.98    1.000
alpha{3}        4.945301    1.169899    3.073457    7.173909    4.856330   1178.78   1203.72    1.000
pinvar{all}     0.303807    0.000923    0.246006    0.366706    0.305088    982.38   1025.22    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	-8511.629082
Model 2: PositiveSelection	-8502.348666
Model 0: one-ratio	-8569.193768
Model 3: discrete	-8500.575061
Model 7: beta	-8516.270802
Model 8: beta&w>1	-8501.796788


Model 0 vs 1	115.12937199999942

Model 2 vs 1	18.56083199999921

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

   516 R      1.000**       13.211

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

    89 A      0.522         1.257 +- 0.314
   135 P      0.643         1.336 +- 0.304
   197 Y      0.561         1.243 +- 0.407
   261 V      0.645         1.339 +- 0.290
   281 S      0.596         1.307 +- 0.301
   283 H      0.608         1.314 +- 0.305
   289 F      0.525         1.202 +- 0.437
   316 I      0.608         1.317 +- 0.284
   516 R      0.963*        1.511 +- 0.244
   707 H      0.513         1.194 +- 0.432


Model 8 vs 7	28.948027999998885

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

   516 R      1.000**       12.993

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

    89 A      0.686         1.191 +- 0.480
   135 P      0.849         1.362 +- 0.352
   190 L      0.506         0.947 +- 0.590
   197 Y      0.704         1.187 +- 0.510
   261 V      0.878         1.395 +- 0.305
   274 N      0.503         0.989 +- 0.539
   281 S      0.801         1.314 +- 0.397
   283 H      0.810         1.322 +- 0.391
   289 F      0.648         1.120 +- 0.544
   316 I      0.852         1.371 +- 0.332
   516 R      0.999**       1.503 +- 0.067
   517 T      0.609         1.108 +- 0.512
   692 D      0.549         1.041 +- 0.531
   707 H      0.634         1.106 +- 0.548