--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 09 00:15:38 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/429/Ubr3-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/429/Ubr3-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/429/Ubr3-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/429/Ubr3-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -18645.26        -18661.44
2     -18646.26        -18659.83
--------------------------------------
TOTAL   -18645.64        -18660.93
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/429/Ubr3-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/429/Ubr3-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/429/Ubr3-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}         0.752294    0.001008    0.685192    0.810213    0.751579   1374.21   1437.60    1.003
r(A<->C){all}   0.099342    0.000090    0.081188    0.118443    0.099188    944.52    977.81    1.000
r(A<->G){all}   0.267816    0.000243    0.238631    0.300177    0.267398   1006.48   1053.41    1.000
r(A<->T){all}   0.120314    0.000157    0.096243    0.144908    0.120104    890.66    945.34    1.001
r(C<->G){all}   0.056371    0.000031    0.045320    0.067430    0.056361   1086.42   1164.03    1.001
r(C<->T){all}   0.398654    0.000322    0.366206    0.436027    0.398724    901.22    906.68    1.000
r(G<->T){all}   0.057504    0.000048    0.043744    0.070783    0.057403    760.43    965.18    1.000
pi(A){all}      0.204171    0.000021    0.195254    0.213321    0.204149   1087.34   1118.87    1.000
pi(C){all}      0.300834    0.000026    0.291586    0.311705    0.300896    980.58    994.25    1.000
pi(G){all}      0.293122    0.000027    0.282778    0.303031    0.293131    876.50    934.72    1.000
pi(T){all}      0.201873    0.000020    0.193091    0.210441    0.201952   1071.81   1098.12    1.000
alpha{1,2}      0.099365    0.000067    0.083950    0.115468    0.099438   1238.43   1287.82    1.000
alpha{3}        7.462424    1.936239    5.003414   10.241120    7.318028   1460.69   1469.65    1.000
pinvar{all}     0.363901    0.000449    0.320703    0.402712    0.364180   1331.31   1416.15    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	-16628.678022
Model 2: PositiveSelection	-16628.678022
Model 0: one-ratio	-16804.82328
Model 3: discrete	-16625.890211
Model 7: beta	-16629.89544
Model 8: beta&w>1	-16625.886107


Model 0 vs 1	352.29051600000093

Model 2 vs 1	0.0

Model 8 vs 7	8.018666000003577

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_Ubr3-PA)

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

    21 R      0.952*        0.999
    25 H      0.835         0.904
    27 P      0.841         0.909
    30 E      0.715         0.806
    33 D      0.722         0.812
    55 A      0.921         0.974
    56 P      0.518         0.642
    58 S      0.752         0.835
    62 A      0.617         0.724
    63 G      0.702         0.793
    66 T      0.673         0.770
    67 G      0.625         0.731
    69 G      0.720         0.809
    70 G      0.889         0.948
    71 V      0.901         0.958
    72 A      0.785         0.862
    76 V      0.914         0.968
   105 T      0.985*        1.026
   106 G      0.703         0.795
   107 P      0.621         0.727
   108 T      0.674         0.771
   110 T      0.521         0.644
   111 T      0.975*        1.018
   112 S      0.968*        1.012
   113 S      0.774         0.854
   114 G      0.985*        1.026
   115 T      0.922         0.975
   117 A      0.914         0.968
   118 S      0.583         0.695
   317 P      0.644         0.746
   360 A      0.583         0.697
  1082 E      0.691         0.787
  1097 P      0.808         0.882
  1107 G      0.679         0.775
  1210 A      0.611         0.718
  1342 S      0.936         0.986
  1369 K      0.735         0.822
  1405 Q      0.544         0.664
  1540 S      0.503         0.630
  1543 A      0.819         0.891
  1770 T      0.765         0.847
  1836 L      0.568         0.683
  1848 S      0.681         0.777
  1852 S      0.583         0.695
  1855 E      0.507         0.633
  1861 N      0.925         0.977
  1868 Q      0.835         0.904
  1891 V      0.533         0.655
  1912 S      0.513         0.638
  1913 S      0.547         0.666
  1916 G      0.862         0.926
  1917 A      0.686         0.780
  1923 I      0.952*        1.000
  2000 T      0.679         0.775

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_Ubr3-PA)

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

    21 R      0.872         1.385 +- 0.309
    25 H      0.702         1.205 +- 0.468
    27 P      0.715         1.219 +- 0.460
    30 E      0.538         1.022 +- 0.537
    33 D      0.542         1.028 +- 0.535
    55 A      0.859         1.367 +- 0.337
    58 S      0.682         1.157 +- 0.523
    63 G      0.613         1.074 +- 0.559
    66 T      0.576         1.028 +- 0.574
    67 G      0.508         0.945 +- 0.591
    69 G      0.641         1.107 +- 0.546
    70 G      0.805         1.313 +- 0.393
    71 V      0.791         1.302 +- 0.398
    72 A      0.728         1.211 +- 0.492
    76 V      0.847         1.355 +- 0.351
   105 T      0.950*        1.458 +- 0.189
   106 G      0.623         1.085 +- 0.556
   108 T      0.569         1.022 +- 0.574
   111 T      0.926         1.435 +- 0.234
   112 S      0.903         1.415 +- 0.268
   113 S      0.610         1.105 +- 0.513
   114 G      0.950*        1.458 +- 0.189
   115 T      0.865         1.373 +- 0.331
   117 A      0.850         1.358 +- 0.348
   317 P      0.532         0.975 +- 0.585
  1082 E      0.513         0.993 +- 0.543
  1097 P      0.661         1.161 +- 0.490
  1107 G      0.580         1.034 +- 0.571
  1342 S      0.876         1.386 +- 0.313
  1369 K      0.541         1.029 +- 0.532
  1543 A      0.683         1.185 +- 0.480
  1770 T      0.594         1.088 +- 0.518
  1848 S      0.581         1.036 +- 0.571
  1861 N      0.783         1.300 +- 0.392
  1868 Q      0.716         1.219 +- 0.461
  1916 G      0.758         1.263 +- 0.432
  1917 A      0.588         1.044 +- 0.568
  1923 I      0.861         1.375 +- 0.320
  2000 T      0.573         1.026 +- 0.572