--- 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