--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Oct 28 01:33:26 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/Ebola_B1_2/VP35/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1_2/VP35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1_2/VP35/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/Ebola_B1_2/VP35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -5986.58         -6035.36
2      -5984.66         -6041.34
--------------------------------------
TOTAL    -5985.21         -6040.65
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1_2/VP35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1_2/VP35/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/Ebola_B1_2/VP35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         4.707892    0.117704    4.060654    5.374117    4.689819    502.21    503.12    1.000
r(A<->C){all}   0.099672    0.000201    0.071524    0.126818    0.099985    660.12    688.56    1.005
r(A<->G){all}   0.371602    0.000773    0.319848    0.428399    0.371649    553.06    575.13    1.000
r(A<->T){all}   0.061980    0.000146    0.039599    0.085469    0.061478    709.26    795.35    1.001
r(C<->G){all}   0.017052    0.000094    0.000294    0.035115    0.015727    507.82    639.35    1.000
r(C<->T){all}   0.395110    0.000789    0.340850    0.451802    0.394999    548.52    610.03    1.000
r(G<->T){all}   0.054585    0.000163    0.032310    0.081650    0.053617    844.91    904.77    1.000
pi(A){all}      0.329473    0.000108    0.307806    0.348527    0.329738    921.82    971.30    1.000
pi(C){all}      0.230478    0.000090    0.211171    0.248031    0.230472    829.75    875.68    1.001
pi(G){all}      0.200144    0.000078    0.183041    0.216889    0.199955    792.45    904.68    1.000
pi(T){all}      0.239906    0.000088    0.220156    0.257330    0.239858    970.15    984.12    1.001
alpha{1,2}      0.216163    0.000293    0.183874    0.250899    0.214944    944.53   1061.89    1.000
alpha{3}        4.642660    1.034646    2.831330    6.676976    4.537871   1069.81   1285.40    1.000
pinvar{all}     0.018494    0.000168    0.000015    0.042420    0.016337    970.00   1114.27    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	-5315.861443
Model 2: PositiveSelection	-5315.861443
Model 0: one-ratio	-5437.423663
Model 3: discrete	-5271.931481
Model 7: beta	-5273.135006
Model 8: beta&w>1	-5273.135134


Model 0 vs 1	243.1244399999996

Model 2 vs 1	0.0

Model 8 vs 7	2.5599999935366213E-4