--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 18 20:20:39 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/285/Kdm2-PE/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/285/Kdm2-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/285/Kdm2-PE/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/285/Kdm2-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -15096.67        -15115.57
2     -15096.34        -15112.12
--------------------------------------
TOTAL   -15096.49        -15114.91
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/285/Kdm2-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/285/Kdm2-PE/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/285/Kdm2-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.351250    0.002579    1.250763    1.450501    1.350649   1501.00   1501.00    1.000
r(A<->C){all}   0.100754    0.000081    0.083938    0.119266    0.100477   1122.44   1159.98    1.000
r(A<->G){all}   0.216724    0.000168    0.191735    0.241593    0.216321    877.24    977.79    1.001
r(A<->T){all}   0.122187    0.000145    0.099128    0.144804    0.122037    926.01    966.50    1.000
r(C<->G){all}   0.042427    0.000023    0.032886    0.051698    0.042265   1033.79   1041.79    1.000
r(C<->T){all}   0.454331    0.000292    0.420632    0.487794    0.454443    726.27    816.81    1.000
r(G<->T){all}   0.063578    0.000048    0.049908    0.076692    0.063453   1177.45   1179.67    1.000
pi(A){all}      0.215653    0.000035    0.205134    0.227951    0.215594    955.57   1039.09    1.000
pi(C){all}      0.284700    0.000039    0.273115    0.297309    0.284695    839.40   1040.34    1.001
pi(G){all}      0.310071    0.000047    0.296339    0.322642    0.310131    762.99    885.74    1.001
pi(T){all}      0.189575    0.000029    0.179854    0.200889    0.189476    984.44   1010.01    1.000
alpha{1,2}      0.123689    0.000039    0.112074    0.136279    0.123522   1111.33   1306.17    1.000
alpha{3}        6.449675    1.448376    4.354494    8.894667    6.311487   1325.40   1376.87    1.000
pinvar{all}     0.271480    0.000413    0.234253    0.313618    0.271817   1162.87   1214.20    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	-13495.123407
Model 2: PositiveSelection	-13495.123407
Model 0: one-ratio	-13634.385871
Model 3: discrete	-13472.075762
Model 7: beta	-13477.695254
Model 8: beta&w>1	-13472.789692


Model 0 vs 1	278.52492800000255

Model 2 vs 1	0.0

Model 8 vs 7	9.811123999999836

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Kdm2-PE)

            Pr(w>1)     post mean +- SE for w

   581 S      0.536         0.833
   583 G      0.988*        1.299
   816 A      0.878         1.185
   823 N      0.582         0.881
   929 V      0.866         1.173
  1032 S      0.933         1.242

Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Kdm2-PE)

            Pr(w>1)     post mean +- SE for w

   581 S      0.751         1.265 +- 0.420
   583 G      0.975*        1.480 +- 0.126
   586 P      0.737         1.243 +- 0.445
   592 A      0.581         1.080 +- 0.514
   600 G      0.688         1.206 +- 0.451
   605 P      0.598         1.093 +- 0.516
   816 A      0.871         1.390 +- 0.293
   823 N      0.753         1.271 +- 0.412
   929 V      0.891         1.406 +- 0.276
  1032 S      0.937         1.448 +- 0.208