--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Sep 30 16:54:04 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-M/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-M/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-M/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-M/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -1473.01         -1537.17
2      -1477.80         -1553.40
--------------------------------------
TOTAL    -1473.70         -1552.70
--------------------------------------


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

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}        15.769697    1.722057   13.105090   18.212610   15.733120    773.49   1013.24    1.000
r(A<->C){all}   0.038430    0.000179    0.014557    0.064083    0.036892    509.63    532.50    1.000
r(A<->G){all}   0.159916    0.001654    0.083393    0.240522    0.155462    268.59    273.48    1.001
r(A<->T){all}   0.057308    0.000372    0.022325    0.094281    0.054990    457.14    529.32    1.000
r(C<->G){all}   0.031517    0.000166    0.009225    0.056913    0.029861    624.50    654.68    1.003
r(C<->T){all}   0.662931    0.003222    0.551174    0.774382    0.665339    256.58    257.26    1.000
r(G<->T){all}   0.049898    0.000370    0.015740    0.086891    0.047543    422.72    497.18    1.000
pi(A){all}      0.269931    0.000754    0.215175    0.320818    0.269214    632.69    725.80    1.004
pi(C){all}      0.279514    0.000607    0.232070    0.328321    0.279575    578.05    662.13    1.001
pi(G){all}      0.234634    0.000647    0.186939    0.284106    0.233310    761.46    774.07    1.000
pi(T){all}      0.215921    0.000465    0.174092    0.256453    0.215094    888.98    931.98    1.000
alpha{1,2}      0.091815    0.000033    0.081070    0.103136    0.091334    621.75    754.25    1.000
alpha{3}        0.356685    0.001297    0.297301    0.429285    0.352270    922.53    939.47    1.001
pinvar{all}     0.111212    0.003561    0.000106    0.214618    0.108030    841.49   1000.73    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	-1065.490048
Model 2: PositiveSelection	-1065.489532
Model 0: one-ratio	-1065.489532
Model 3: discrete	-1065.489532
Model 7: beta	-1065.675108
Model 8: beta&w>1	-1065.675727


Model 0 vs 1	0.0010319999996681872

Model 2 vs 1	0.0010319999996681872

Model 8 vs 7	0.0012380000002849556