--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Oct 06 22:59:35 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=/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/B3_A/Zika-NS4B_3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_3/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/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3259.86         -3359.88
2      -3271.49         -3357.62
--------------------------------------
TOTAL    -3260.56         -3359.29
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_3/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/B3_A/Zika-NS4B_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}        16.297712    2.385388   13.119120   19.065950   16.292040    293.92    374.73    1.003
r(A<->C){all}   0.024798    0.000071    0.010034    0.042033    0.024099    346.64    388.90    1.001
r(A<->G){all}   0.231548    0.003217    0.113716    0.329417    0.237929    110.39    133.88    1.004
r(A<->T){all}   0.056773    0.000199    0.029493    0.083506    0.055901    324.85    370.05    1.001
r(C<->G){all}   0.010469    0.000030    0.001605    0.021235    0.009555    528.24    542.75    1.000
r(C<->T){all}   0.649993    0.004824    0.535716    0.799492    0.639936     99.48    120.42    1.004
r(G<->T){all}   0.026419    0.000096    0.008932    0.046072    0.025178    143.57    282.29    1.001
pi(A){all}      0.259620    0.000233    0.230796    0.288708    0.259513    844.12    886.73    1.000
pi(C){all}      0.254255    0.000200    0.228274    0.283310    0.254509    761.44    794.63    1.000
pi(G){all}      0.262438    0.000233    0.231487    0.290401    0.262483    587.99    606.32    1.000
pi(T){all}      0.223686    0.000181    0.197806    0.249775    0.223213    693.39    707.42    1.001
alpha{1,2}      0.071008    0.000011    0.064773    0.077572    0.070856    281.06    368.08    1.003
alpha{3}        0.264338    0.000268    0.234235    0.297281    0.263165    722.38    800.07    1.000
pinvar{all}     0.326829    0.002141    0.238028    0.418578    0.328881    207.31    282.37    1.002
------------------------------------------------------------------------------------------------------
* 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	-2716.8929
Model 2: PositiveSelection	-2716.8929
Model 0: one-ratio	-2738.892858
Model 3: discrete	-2716.715815
Model 7: beta	-2719.632129
Model 8: beta&w>1	-2719.634455


Model 0 vs 1	43.99991600000067

Model 2 vs 1	0.0

Model 8 vs 7	0.004651999999623513