--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 02 22:49:08 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/85/CG15822-PG/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/85/CG15822-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/85/CG15822-PG/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/85/CG15822-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -15778.15        -15793.52
2     -15777.77        -15793.97
--------------------------------------
TOTAL   -15777.94        -15793.77
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/85/CG15822-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/85/CG15822-PG/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/85/CG15822-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.123199    0.001954    1.036276    1.207578    1.121198   1223.19   1302.27    1.000
r(A<->C){all}   0.106953    0.000073    0.090548    0.123605    0.106671    988.32    989.48    1.000
r(A<->G){all}   0.253741    0.000200    0.224834    0.280489    0.253666    913.84    924.36    1.001
r(A<->T){all}   0.100279    0.000102    0.079559    0.118974    0.099839    984.77   1033.52    1.001
r(C<->G){all}   0.075287    0.000040    0.063225    0.088279    0.075254   1015.29   1033.14    1.000
r(C<->T){all}   0.401858    0.000290    0.368504    0.435083    0.401580    825.37    874.72    1.000
r(G<->T){all}   0.061883    0.000048    0.048795    0.075169    0.061826    786.29    883.60    1.001
pi(A){all}      0.228295    0.000038    0.216492    0.240658    0.228237    778.32    802.50    1.000
pi(C){all}      0.285774    0.000044    0.273315    0.298624    0.285823    991.61   1018.75    1.000
pi(G){all}      0.301789    0.000045    0.288194    0.314498    0.301844   1183.55   1184.64    1.001
pi(T){all}      0.184142    0.000031    0.172799    0.194450    0.184160    920.44   1081.27    1.001
alpha{1,2}      0.217141    0.000228    0.189676    0.248082    0.216458   1161.13   1264.81    1.000
alpha{3}        4.126773    0.715178    2.626800    5.848609    4.021962   1274.90   1387.95    1.000
pinvar{all}     0.380077    0.000475    0.337407    0.421851    0.380431   1141.89   1275.68    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	-14278.364164
Model 2: PositiveSelection	-14278.364165
Model 0: one-ratio	-14586.342621
Model 3: discrete	-14254.990939
Model 7: beta	-14261.142299
Model 8: beta&w>1	-14255.199834


Model 0 vs 1	615.9569139999985

Model 2 vs 1	2.0000006770715117E-6

Model 8 vs 7	11.884930000000168

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_CG15822-PG)

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

   247 G      0.641         1.343
   254 G      0.930         1.702
   795 A      0.871         1.629
   798 S      0.895         1.658
   881 S      0.980*        1.764
   969 L      0.703         1.420
  1018 N      0.611         1.305
  1026 G      0.685         1.397
  1182 L      0.967*        1.748
  1197 T      0.649         1.351

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_CG15822-PG)

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

   173 A      0.524         1.011 +- 0.535
   247 G      0.920         1.434 +- 0.229
   252 S      0.666         1.170 +- 0.484
   253 A      0.776         1.285 +- 0.412
   254 G      0.977*        1.482 +- 0.117
   377 S      0.795         1.311 +- 0.382
   380 M      0.817         1.343 +- 0.339
   518 H      0.555         1.071 +- 0.497
   607 P      0.797         1.314 +- 0.378
   609 R      0.726         1.254 +- 0.413
   610 S      0.718         1.224 +- 0.455
   612 S      0.627         1.145 +- 0.476
   614 S      0.748         1.274 +- 0.400
   767 Q      0.749         1.274 +- 0.401
   784 V      0.666         1.184 +- 0.461
   787 G      0.530         1.022 +- 0.530
   788 E      0.700         1.219 +- 0.443
   789 N      0.872         1.389 +- 0.296
   795 A      0.965*        1.473 +- 0.145
   796 A      0.876         1.393 +- 0.291
   797 Y      0.741         1.260 +- 0.418
   798 S      0.969*        1.475 +- 0.141
   807 S      0.593         1.110 +- 0.487
   836 G      0.553         1.068 +- 0.499
   838 G      0.593         1.090 +- 0.515
   870 L      0.508         0.996 +- 0.536
   881 S      0.990*        1.492 +- 0.076
   946 C      0.625         1.144 +- 0.475
   964 I      0.584         1.079 +- 0.519
   969 L      0.932         1.444 +- 0.211
  1016 V      0.769         1.293 +- 0.387
  1018 N      0.912         1.426 +- 0.243
  1021 S      0.699         1.227 +- 0.428
  1026 G      0.926         1.438 +- 0.224
  1101 P      0.854         1.371 +- 0.321
  1119 R      0.611         1.110 +- 0.509
  1182 L      0.985*        1.489 +- 0.091
  1183 A      0.688         1.207 +- 0.450
  1197 T      0.914         1.425 +- 0.250