--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 25 13:35:40 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-PC/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

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

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -1309.29         -1348.08
2      -1310.76         -1347.38
--------------------------------------
TOTAL    -1309.77         -1347.79
--------------------------------------


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

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.765111    0.166174    0.148443    1.551500    0.690985    660.91    696.87    1.000
r(A<->C){all}   0.075164    0.001965    0.005343    0.160495    0.068080    308.73    368.35    1.000
r(A<->G){all}   0.181657    0.012948    0.020501    0.414235    0.158441    207.47    216.11    1.000
r(A<->T){all}   0.053634    0.001680    0.000088    0.131582    0.044321    383.12    430.90    1.000
r(C<->G){all}   0.044690    0.000961    0.000066    0.105612    0.037496    450.69    470.50    1.001
r(C<->T){all}   0.624717    0.022601    0.348430    0.907682    0.630729    173.95    179.98    1.000
r(G<->T){all}   0.020138    0.000453    0.000024    0.063515    0.013388    359.28    411.36    1.001
pi(A){all}      0.287291    0.000265    0.257842    0.321432    0.287098   1195.79   1230.81    1.000
pi(C){all}      0.257272    0.000258    0.224178    0.287263    0.256994   1068.78   1205.46    1.000
pi(G){all}      0.257247    0.000261    0.227363    0.289712    0.257252   1159.19   1201.43    1.000
pi(T){all}      0.198191    0.000207    0.171397    0.226982    0.198188   1180.63   1304.12    1.000
alpha{1,2}      0.089389    0.000597    0.049461    0.138820    0.085504    924.19   1066.04    1.000
alpha{3}        0.783188    0.264595    0.089797    1.808021    0.655387    677.42    804.51    1.000
pinvar{all}     0.853751    0.000916    0.794113    0.906563    0.858097    827.73    927.03    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	-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