--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Oct 05 23:13:37 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_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_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/B2_A/Zika-NS1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -4271.55         -4351.50
2      -4231.87         -4318.87
--------------------------------------
TOTAL    -4232.56         -4350.81
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_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/B2_A/Zika-NS1_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}        14.769727    2.145047   11.862030   17.608370   14.774270     81.84    409.42    1.099
r(A<->C){all}   0.012013    0.000139    0.000018    0.031625    0.007175    116.60    212.98    2.887
r(A<->G){all}   0.082452    0.006760    0.004091    0.219470    0.063264     47.32     78.74    2.963
r(A<->T){all}   0.013605    0.000162    0.000686    0.035950    0.005918    147.50    198.28    2.629
r(C<->G){all}   0.003862    0.000018    0.000030    0.012404    0.001571    303.35    434.38    1.737
r(C<->T){all}   0.877249    0.013642    0.692226    0.991926    0.979559     44.11     76.24    3.418
r(G<->T){all}   0.010819    0.000102    0.000493    0.029233    0.005115     74.42    163.35    2.410
pi(A){all}      0.294127    0.000198    0.268270    0.322398    0.293968    556.51    715.78    1.069
pi(C){all}      0.212284    0.000138    0.189922    0.235044    0.212283    214.77    536.77    1.034
pi(G){all}      0.292090    0.000181    0.266072    0.318648    0.291899    281.80    556.00    1.032
pi(T){all}      0.201498    0.000135    0.179705    0.224763    0.201183    221.00    633.56    1.090
alpha{1,2}      0.066671    0.000029    0.056684    0.076392    0.066585    202.78    264.51    1.985
alpha{3}        0.407146    0.023621    0.228882    0.601040    0.471867    121.07    253.20   10.499
pinvar{all}     0.333347    0.003594    0.234196    0.443611    0.330952    348.12    723.05    2.187
------------------------------------------------------------------------------------------------------
* 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	-3631.898993
Model 2: PositiveSelection	-3631.898992
Model 0: one-ratio	-3637.596052
Model 3: discrete	-3629.469799
Model 7: beta	-3629.644731
Model 8: beta&w>1	-3629.644885


Model 0 vs 1	11.394118000000162

Model 2 vs 1	1.99999976757681E-6

Model 8 vs 7	3.080000005866168E-4