--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Feb 18 16:59:54 WET 2016
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/B4_A/Zika-NS5_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_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/B4_A/Zika-NS5_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -9092.17         -9173.46
2      -9087.97         -9190.61
--------------------------------------
TOTAL    -9088.65         -9189.91
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_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/B4_A/Zika-NS5_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}         1.082852    0.003223    0.973582    1.197589    1.080876    459.88    477.61    1.000
r(A<->C){all}   0.022532    0.000018    0.014307    0.031134    0.022322    814.98    908.29    1.000
r(A<->G){all}   0.219084    0.000443    0.179541    0.259466    0.217997    413.71    444.60    1.000
r(A<->T){all}   0.027275    0.000030    0.017051    0.037932    0.026899    733.37    739.62    1.002
r(C<->G){all}   0.006560    0.000006    0.002064    0.011187    0.006269    682.25    705.63    1.000
r(C<->T){all}   0.704344    0.000579    0.660163    0.752669    0.705359    329.62    370.40    1.000
r(G<->T){all}   0.020206    0.000020    0.011900    0.029312    0.019950    543.81    643.98    1.001
pi(A){all}      0.279823    0.000063    0.264921    0.295600    0.279672    844.22    898.85    1.000
pi(C){all}      0.227426    0.000052    0.213801    0.241997    0.227649    654.10    709.96    1.000
pi(G){all}      0.295871    0.000066    0.280237    0.311779    0.295871    886.94    890.36    1.003
pi(T){all}      0.196880    0.000046    0.183018    0.210027    0.196781    807.42    888.73    1.000
alpha{1,2}      0.109801    0.000078    0.093189    0.127740    0.109636   1111.52   1175.65    1.001
alpha{3}        4.898783    1.062486    3.077460    6.942204    4.789856   1116.79   1204.92    1.000
pinvar{all}     0.266643    0.000915    0.206271    0.325327    0.267805    927.39    985.31    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	-8491.066751
Model 2: PositiveSelection	-8491.066747
Model 0: one-ratio	-8538.702434
Model 3: discrete	-8487.233605
Model 7: beta	-8487.588366
Model 8: beta&w>1	-8487.590316


Model 0 vs 1	95.27136600000085

Model 2 vs 1	7.99999907030724E-6

Model 8 vs 7	0.003899999999703141