--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Nov 24 23:08:22 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/30/CadN-PB/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/30/CadN-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/30/CadN-PB/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/30/CadN-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -31081.84        -31099.68
2     -31081.51        -31096.19
--------------------------------------
TOTAL   -31081.66        -31099.02
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/30/CadN-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/30/CadN-PB/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/30/CadN-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.188971    0.000973    1.126296    1.246559    1.188715   1309.44   1405.22    1.000
r(A<->C){all}   0.082034    0.000030    0.071656    0.092787    0.081819    863.83   1042.38    1.000
r(A<->G){all}   0.295364    0.000114    0.274008    0.316136    0.295474    694.39    787.27    1.000
r(A<->T){all}   0.069289    0.000027    0.059743    0.079959    0.069227   1119.18   1131.53    1.001
r(C<->G){all}   0.057160    0.000019    0.048391    0.065358    0.057059   1151.27   1201.67    1.000
r(C<->T){all}   0.443380    0.000125    0.421869    0.465118    0.443282    702.87    726.36    1.000
r(G<->T){all}   0.052773    0.000019    0.044629    0.061336    0.052698   1177.02   1184.63    1.000
pi(A){all}      0.255058    0.000018    0.246878    0.263660    0.255086    750.24    798.92    1.000
pi(C){all}      0.259919    0.000017    0.252287    0.268267    0.259967    942.73    966.27    1.000
pi(G){all}      0.267007    0.000018    0.258202    0.274670    0.266977    697.19    750.73    1.000
pi(T){all}      0.218016    0.000014    0.210805    0.225699    0.217993    647.38    815.33    1.000
alpha{1,2}      0.084621    0.000008    0.079028    0.090452    0.084532   1280.40   1338.59    1.001
alpha{3}        8.223141    1.646335    5.806509   10.680550    8.115795   1501.00   1501.00    1.000
pinvar{all}     0.440763    0.000115    0.422100    0.463544    0.440699   1341.46   1421.23    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	-28885.813829
Model 2: PositiveSelection	-28885.813957
Model 0: one-ratio	-28957.23396
Model 3: discrete	-28855.086416
Model 7: beta	-28869.054419
Model 8: beta&w>1	-28865.561435


Model 0 vs 1	142.84026200000517

Model 2 vs 1	2.5599999935366213E-4

Model 8 vs 7	6.985968000000867

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
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_CadN-PB)

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

    33 F      0.657         1.160 +- 0.492
  2303 S      0.669         1.188 +- 0.461