--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Oct 08 06:02:51 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/B2_A/Zika-NS1_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_4/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/B2_A/Zika-NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -4251.85         -4338.35
2      -4251.76         -4335.80
--------------------------------------
TOTAL    -4251.80         -4337.73
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_4/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/B2_A/Zika-NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}        16.204429    2.763839   12.793460   19.258120   16.249460    177.22    180.94    1.022
r(A<->C){all}   0.031193    0.000076    0.016078    0.049308    0.030296    198.60    214.43    1.005
r(A<->G){all}   0.210437    0.002583    0.096297    0.294179    0.218719     57.20     68.60    1.046
r(A<->T){all}   0.031975    0.000089    0.015497    0.051734    0.031330    148.51    179.81    1.012
r(C<->G){all}   0.007503    0.000017    0.000916    0.015475    0.006895    660.84    722.23    1.000
r(C<->T){all}   0.694252    0.003821    0.593376    0.836197    0.682576     51.17     63.36    1.048
r(G<->T){all}   0.024640    0.000061    0.009547    0.039124    0.023998    238.79    248.35    1.011
pi(A){all}      0.286575    0.000185    0.259524    0.311500    0.286354    675.91    795.45    1.005
pi(C){all}      0.210384    0.000121    0.189323    0.231898    0.209933    740.98    798.58    1.002
pi(G){all}      0.298313    0.000178    0.271243    0.323495    0.297991    547.88    694.98    1.000
pi(T){all}      0.204727    0.000118    0.182902    0.225058    0.204593    942.11    961.54    1.000
alpha{1,2}      0.069273    0.000011    0.063215    0.075482    0.069039    146.69    177.51    1.018
alpha{3}        0.252505    0.000182    0.226996    0.279545    0.251704    351.32    429.96    1.000
pinvar{all}     0.409235    0.001561    0.328038    0.483098    0.411992    114.94    133.66    1.020
------------------------------------------------------------------------------------------------------
* 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	-3497.189929
Model 2: PositiveSelection	-3497.190052
Model 0: one-ratio	-3501.803461
Model 3: discrete	-3489.842715
Model 7: beta	-3490.529667
Model 8: beta&w>1	-3490.530396


Model 0 vs 1	9.2270639999997

Model 2 vs 1	2.459999996062834E-4

Model 8 vs 7	0.0014580000006390037