--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Oct 06 09:55:26 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_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_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/B3_A/Zika-NS4B_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3502.25         -3612.69
2      -3509.91         -3627.76
--------------------------------------
TOTAL    -3502.94         -3627.06
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_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/B3_A/Zika-NS4B_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}        13.892731    2.556904   10.971420   17.102380   13.786470     14.31     47.95    1.147
r(A<->C){all}   0.012176    0.000126    0.001041    0.033276    0.005110      4.97      9.11    1.456
r(A<->G){all}   0.100693    0.010644    0.010608    0.277797    0.024105      4.02      7.87    1.503
r(A<->T){all}   0.021531    0.000397    0.002084    0.056989    0.008299      4.58      8.78    1.448
r(C<->G){all}   0.004746    0.000027    0.000003    0.015489    0.002032      7.12     10.60    1.306
r(C<->T){all}   0.852714    0.020393    0.616312    0.980607    0.959244      3.88      7.77    1.512
r(G<->T){all}   0.008139    0.000063    0.000638    0.024472    0.003686      6.79     10.60    1.384
pi(A){all}      0.257153    0.000212    0.229895    0.285269    0.256978    337.02    583.51    1.000
pi(C){all}      0.254620    0.000204    0.226931    0.283140    0.254973    460.86    578.83    1.005
pi(G){all}      0.260478    0.000226    0.232317    0.291663    0.260072    455.76    478.18    1.017
pi(T){all}      0.227749    0.000186    0.202969    0.255321    0.227727    215.02    278.30    1.005
alpha{1,2}      0.072840    0.000017    0.065347    0.081024    0.072772     11.77     55.86    1.105
alpha{3}        0.434918    0.024610    0.261500    0.670959    0.335564      5.77     16.21    1.245
pinvar{all}     0.190342    0.005976    0.016859    0.311045    0.199249      6.88     18.48    1.183
------------------------------------------------------------------------------------------------------
* 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	-2973.91438
Model 2: PositiveSelection	-2973.91438
Model 0: one-ratio	-3016.220865
Model 3: discrete	-2973.800255
Model 7: beta	-2978.040516
Model 8: beta&w>1	-2978.042225


Model 0 vs 1	84.61296999999922

Model 2 vs 1	0.0

Model 8 vs 7	0.003418000000237953