--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Dec 05 05:03:59 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/361/qkr58E-1-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/361/qkr58E-1-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/361/qkr58E-1-PA/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/361/qkr58E-1-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3780.46         -3797.08
2      -3781.36         -3799.64
--------------------------------------
TOTAL    -3780.81         -3799.02
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/361/qkr58E-1-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/361/qkr58E-1-PA/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/361/qkr58E-1-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.065359    0.006915    0.912972    1.234227    1.061439   1138.71   1251.21    1.000
r(A<->C){all}   0.084524    0.000215    0.057291    0.114546    0.083660    979.43    984.54    1.001
r(A<->G){all}   0.276967    0.000970    0.215801    0.335960    0.275847    754.18    874.83    1.000
r(A<->T){all}   0.096056    0.000643    0.048911    0.145515    0.094425    902.23    918.51    1.001
r(C<->G){all}   0.032987    0.000056    0.017822    0.047004    0.032502    785.38    911.57    1.000
r(C<->T){all}   0.454792    0.001279    0.385721    0.522934    0.455275    747.79    881.13    1.000
r(G<->T){all}   0.054675    0.000200    0.030181    0.084598    0.053848   1147.23   1161.36    1.000
pi(A){all}      0.258130    0.000153    0.230932    0.279456    0.257988   1126.00   1146.05    1.000
pi(C){all}      0.313262    0.000161    0.288246    0.337793    0.312989   1147.90   1223.30    1.001
pi(G){all}      0.261711    0.000149    0.239230    0.286174    0.261419   1067.67   1083.76    1.000
pi(T){all}      0.166896    0.000095    0.148178    0.186131    0.166617   1114.44   1118.16    1.000
alpha{1,2}      0.067527    0.000450    0.011598    0.096363    0.073010   1099.57   1120.10    1.002
alpha{3}        4.120022    1.027653    2.304547    6.102269    3.991260   1323.96   1392.79    1.001
pinvar{all}     0.366686    0.001423    0.288469    0.435804    0.366860   1126.31   1179.58    1.002
------------------------------------------------------------------------------------------------------
* 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	-3489.220768
Model 2: PositiveSelection	-3489.218787
Model 0: one-ratio	-3489.218787
Model 3: discrete	-3488.479275
Model 7: beta	-3488.491923
Model 8: beta&w>1	-3488.495866


Model 0 vs 1	0.003962000000683474

Model 2 vs 1	0.003962000000683474

Model 8 vs 7	0.007886000000326021