--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 25 14:09:41 WET 2016
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/1/14-3-3zeta-PF/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/1/14-3-3zeta-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/14-3-3zeta-PF/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/1/14-3-3zeta-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -1309.54         -1349.51
2      -1309.56         -1346.69
--------------------------------------
TOTAL    -1309.55         -1348.87
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/1/14-3-3zeta-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/14-3-3zeta-PF/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/1/14-3-3zeta-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.773171    0.183746    0.131319    1.555523    0.690411    663.42    688.18    1.000
r(A<->C){all}   0.076535    0.002012    0.001789    0.161277    0.069540    462.70    489.46    1.001
r(A<->G){all}   0.184582    0.011134    0.020620    0.390947    0.167742    212.49    231.45    1.002
r(A<->T){all}   0.057489    0.001708    0.000097    0.134465    0.048918    377.68    445.33    1.004
r(C<->G){all}   0.047575    0.001074    0.000793    0.112710    0.040204    431.71    433.92    1.001
r(C<->T){all}   0.612294    0.021431    0.353034    0.902968    0.619312    213.30    224.03    1.002
r(G<->T){all}   0.021526    0.000482    0.000014    0.064504    0.014852    601.31    750.46    1.000
pi(A){all}      0.287230    0.000269    0.256960    0.320471    0.286909   1068.07   1074.44    1.000
pi(C){all}      0.257498    0.000247    0.227803    0.288917    0.257218   1026.46   1151.09    1.000
pi(G){all}      0.257149    0.000252    0.225835    0.287693    0.257058   1164.42   1248.35    1.000
pi(T){all}      0.198123    0.000200    0.170892    0.225212    0.197553   1054.69   1148.15    1.000
alpha{1,2}      0.088992    0.000625    0.051868    0.147356    0.085145    599.85    891.91    1.000
alpha{3}        0.762185    0.259295    0.077749    1.735662    0.631283    704.62    757.91    1.000
pinvar{all}     0.853421    0.001031    0.787751    0.908532    0.857633    767.83    969.32    1.001
------------------------------------------------------------------------------------------------------
* 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	-1225.465062
Model 2: PositiveSelection	-1225.456381
Model 0: one-ratio	-1226.517883
Model 3: discrete	-1225.456381
Model 7: beta	-1225.818465
Model 8: beta&w>1	-1225.456377


Model 0 vs 1	2.105641999999989

Model 2 vs 1	0.017362000000048283

Model 8 vs 7	0.7241760000001705