--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Feb 13 13:01:50 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_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -9221.12         -9313.56
2      -9222.38         -9318.18
--------------------------------------
TOTAL    -9221.56         -9317.50
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.086105    0.003582    0.970288    1.200607    1.084150    243.81    452.44    1.000
r(A<->C){all}   0.023797    0.000021    0.015474    0.032980    0.023493    686.89    725.34    1.000
r(A<->G){all}   0.185831    0.000328    0.152072    0.219957    0.185444    336.50    343.67    1.002
r(A<->T){all}   0.025585    0.000027    0.015881    0.035774    0.025256    561.72    602.54    1.000
r(C<->G){all}   0.006772    0.000006    0.002605    0.011406    0.006540    839.77    843.92    1.001
r(C<->T){all}   0.737604    0.000456    0.697050    0.777824    0.737535    290.23    321.07    1.001
r(G<->T){all}   0.020410    0.000020    0.012347    0.029152    0.020211    646.78    671.52    1.000
pi(A){all}      0.281247    0.000065    0.266327    0.297671    0.281022    642.89    783.45    1.003
pi(C){all}      0.229648    0.000047    0.215688    0.242565    0.229772    726.08    880.50    1.000
pi(G){all}      0.293509    0.000064    0.278802    0.309439    0.293509    755.10    780.12    1.001
pi(T){all}      0.195595    0.000044    0.183774    0.209850    0.195312    835.94    933.52    1.000
alpha{1,2}      0.124226    0.000080    0.107248    0.142570    0.123852    772.87    946.53    1.000
alpha{3}        4.775503    1.087070    2.830874    6.864657    4.632361   1181.58   1203.17    1.000
pinvar{all}     0.275870    0.000839    0.220134    0.331123    0.276253    976.78    997.42    1.001
------------------------------------------------------------------------------------------------------
* 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	-8681.39429
Model 2: PositiveSelection	-8670.732763
Model 0: one-ratio	-8741.56394
Model 3: discrete	-8664.850351
Model 7: beta	-8681.346316
Model 8: beta&w>1	-8664.695611


Model 0 vs 1	120.33929999999964

Model 2 vs 1	21.32305400000041

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:KY272987|Organism:Zika virus|Strain Name:SI-BKK01|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)

            Pr(w>1)     post mean +- SE for w

   517 R      1.000**       13.998

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:KY272987|Organism:Zika virus|Strain Name:SI-BKK01|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)

            Pr(w>1)     post mean +- SE for w

    73 Y      0.502         1.182 +- 0.460
   200 Y      0.651         1.351 +- 0.352
   277 N      0.516         1.266 +- 0.284
   284 S      0.642         1.344 +- 0.309
   286 H      0.597         1.313 +- 0.324
   292 F      0.512         1.194 +- 0.456
   517 R      0.974*        1.540 +- 0.415
   564 Q      0.508         1.189 +- 0.461
   814 T      0.603         1.320 +- 0.302


Model 8 vs 7	33.30141000000003

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:KY272987|Organism:Zika virus|Strain Name:SI-BKK01|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)

            Pr(w>1)     post mean +- SE for w

   517 R      1.000**       13.585

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:KY272987|Organism:Zika virus|Strain Name:SI-BKK01|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)

            Pr(w>1)     post mean +- SE for w

    73 Y      0.613         1.080 +- 0.563
   138 P      0.566         1.023 +- 0.578
   200 Y      0.856         1.371 +- 0.352
   277 N      0.732         1.254 +- 0.432
   284 S      0.877         1.397 +- 0.313
   286 H      0.796         1.311 +- 0.408
   292 F      0.628         1.098 +- 0.557
   517 R      0.999**       1.507 +- 0.090
   564 Q      0.620         1.089 +- 0.561
   702 H      0.581         1.042 +- 0.573
   814 T      0.839         1.360 +- 0.352