--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Oct 08 03:47:30 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_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3609.72         -3705.56
2      -3613.01         -3706.65
--------------------------------------
TOTAL    -3610.38         -3706.25
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}        15.264623    2.282281   12.350370   18.298370   15.248630    528.91    572.09    1.000
r(A<->C){all}   0.023677    0.000056    0.010464    0.038767    0.022949    644.03    740.61    1.001
r(A<->G){all}   0.242827    0.001936    0.148156    0.325439    0.244216    193.16    221.31    1.000
r(A<->T){all}   0.059445    0.000162    0.035405    0.083768    0.058813    476.21    477.24    1.000
r(C<->G){all}   0.012366    0.000032    0.003160    0.024003    0.011492    381.21    483.88    1.000
r(C<->T){all}   0.632217    0.002760    0.534817    0.742530    0.629648    183.95    215.00    1.000
r(G<->T){all}   0.029469    0.000083    0.013396    0.048432    0.028410    501.36    526.26    1.000
pi(A){all}      0.263622    0.000224    0.233116    0.291366    0.263681    732.51    849.29    1.000
pi(C){all}      0.250307    0.000186    0.224573    0.276967    0.250425    918.74    921.18    1.000
pi(G){all}      0.259313    0.000215    0.231060    0.287604    0.259242    650.75    796.15    1.000
pi(T){all}      0.226758    0.000181    0.199632    0.251982    0.226721    832.25    840.18    1.000
alpha{1,2}      0.076450    0.000012    0.069776    0.083272    0.076277    829.98    847.73    1.000
alpha{3}        0.305445    0.000587    0.263908    0.354637    0.302732    565.99    601.20    1.000
pinvar{all}     0.292154    0.001639    0.211599    0.366891    0.293969    667.64    709.60    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	-3235.201478
Model 2: PositiveSelection	-3235.176513
Model 0: one-ratio	-3277.003946
Model 3: discrete	-3234.226796
Model 7: beta	-3235.963243
Model 8: beta&w>1	-3235.963784


Model 0 vs 1	83.60493599999973

Model 2 vs 1	0.04993000000013126

Model 8 vs 7	0.001081999999769323