--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Sep 30 21:18:16 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=
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-NS4A/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-NS4A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-NS4A/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/Batch_1_ADOPS/Zika-NS4A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -1770.42         -1847.99
2      -1781.33         -1844.87
--------------------------------------
TOTAL    -1771.11         -1847.34
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-NS4A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-NS4A/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/Batch_1_ADOPS/Zika-NS4A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}        13.276222    1.477160   10.999750   15.664800   13.249460    996.68   1024.76    1.000
r(A<->C){all}   0.032708    0.000185    0.011352    0.060066    0.030292    427.16    450.40    1.000
r(A<->G){all}   0.125645    0.002135    0.054468    0.226234    0.115532    221.49    257.69    1.000
r(A<->T){all}   0.019681    0.000116    0.002481    0.040766    0.017953    342.23    409.88    1.000
r(C<->G){all}   0.008553    0.000027    0.000598    0.018280    0.007590    630.20    721.05    1.002
r(C<->T){all}   0.805026    0.003663    0.669135    0.899584    0.815784    217.40    260.09    1.000
r(G<->T){all}   0.008387    0.000033    0.000009    0.019281    0.007124    622.20    703.86    1.000
pi(A){all}      0.230422    0.000384    0.193433    0.269012    0.229969    821.78    848.36    1.002
pi(C){all}      0.236246    0.000330    0.202710    0.272727    0.236391    924.96   1022.55    1.001
pi(G){all}      0.303681    0.000472    0.264109    0.348127    0.303157    812.18    842.32    1.000
pi(T){all}      0.229651    0.000338    0.194477    0.265779    0.229456    820.40    847.38    1.000
alpha{1,2}      0.086537    0.000035    0.074815    0.097720    0.086130    808.99    973.05    1.000
alpha{3}        0.341138    0.010658    0.235984    0.608174    0.306821    213.73    328.97    1.000
pinvar{all}     0.335177    0.002892    0.234339    0.443935    0.334452    672.18    847.91    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	-1430.147849
Model 2: PositiveSelection	-1430.147849
Model 0: one-ratio	-1430.877046
Model 3: discrete	-1428.604927
Model 7: beta	-1428.679144
Model 8: beta&w>1	-1428.679412


Model 0 vs 1	1.4583940000002258

Model 2 vs 1	0.0

Model 8 vs 7	5.360000000109721E-4