--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Oct 05 23:37:12 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_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3415.01         -3502.53
2      -3408.77         -3509.13
--------------------------------------
TOTAL    -3409.46         -3508.44
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}        15.101058    1.771210   12.543350   17.713610   15.053870    365.53    665.69    1.001
r(A<->C){all}   0.019764    0.000052    0.006825    0.033594    0.018879    252.24    295.90    1.000
r(A<->G){all}   0.182177    0.002173    0.108438    0.281746    0.172486    109.30    117.77    1.004
r(A<->T){all}   0.039531    0.000115    0.021553    0.061335    0.038335    231.55    337.67    1.003
r(C<->G){all}   0.003496    0.000009    0.000001    0.009521    0.002692    459.03    495.23    1.007
r(C<->T){all}   0.734913    0.003181    0.617848    0.828604    0.743729    103.77    114.71    1.006
r(G<->T){all}   0.020120    0.000052    0.006988    0.034403    0.019212    206.78    376.46    1.013
pi(A){all}      0.261451    0.000225    0.233679    0.291664    0.261674    838.56    933.51    1.000
pi(C){all}      0.252563    0.000199    0.223881    0.279417    0.252300    946.30    965.98    1.000
pi(G){all}      0.260868    0.000224    0.231771    0.290070    0.260537    828.43    859.92    1.000
pi(T){all}      0.225118    0.000177    0.199206    0.250935    0.224682    560.44    667.67    1.000
alpha{1,2}      0.073438    0.000010    0.067709    0.079962    0.073309    403.54    435.66    1.001
alpha{3}        0.282344    0.000418    0.243481    0.322988    0.280347    346.93    555.10    1.003
pinvar{all}     0.262039    0.001768    0.177148    0.341720    0.261534    443.51    503.98    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	-2917.05587
Model 2: PositiveSelection	-2917.05587
Model 0: one-ratio	-2947.643808
Model 3: discrete	-2915.834153
Model 7: beta	-2917.867125
Model 8: beta&w>1	-2917.867171


Model 0 vs 1	61.175875999999334

Model 2 vs 1	0.0

Model 8 vs 7	9.199999931297498E-5