--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 02 21:43:58 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/96/CG18304-PC/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/96/CG18304-PC/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/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -22674.84        -22691.88
2     -22675.05        -22692.12
--------------------------------------
TOTAL   -22674.94        -22692.01
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/96/CG18304-PC/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/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.378362    0.001783    1.290439    1.457044    1.376656   1235.10   1368.05    1.000
r(A<->C){all}   0.087775    0.000038    0.075997    0.099652    0.087709    663.76    686.03    1.000
r(A<->G){all}   0.246503    0.000116    0.225354    0.267568    0.246621    798.18    855.01    1.000
r(A<->T){all}   0.144655    0.000113    0.125112    0.167140    0.144525    827.04    860.73    1.000
r(C<->G){all}   0.053813    0.000017    0.046109    0.062053    0.053715   1091.83   1139.29    1.000
r(C<->T){all}   0.392110    0.000191    0.366214    0.418865    0.392153    763.73    781.07    1.000
r(G<->T){all}   0.075145    0.000045    0.063069    0.088790    0.074932    875.30    958.96    1.000
pi(A){all}      0.273351    0.000032    0.263216    0.285246    0.273392    768.25    896.44    1.000
pi(C){all}      0.270967    0.000029    0.260474    0.281282    0.270728    866.50    969.68    1.000
pi(G){all}      0.297671    0.000032    0.287441    0.309208    0.297606    909.31    960.24    1.000
pi(T){all}      0.158011    0.000019    0.149258    0.166010    0.157955    560.60    719.01    1.000
alpha{1,2}      0.153716    0.000044    0.141233    0.166938    0.153573   1212.70   1325.04    1.000
alpha{3}        5.058830    0.710990    3.582431    6.711710    4.970144   1285.73   1339.59    1.000
pinvar{all}     0.305418    0.000279    0.273403    0.339705    0.305716   1323.45   1346.14    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	-20645.365115
Model 2: PositiveSelection	-20645.365115
Model 0: one-ratio	-20914.180362
Model 3: discrete	-20570.698627
Model 7: beta	-20577.320931
Model 8: beta&w>1	-20570.437721


Model 0 vs 1	537.6304939999973

Model 2 vs 1	0.0

Model 8 vs 7	13.766419999999925

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_CG18304-PC)

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

   117 S      0.584         0.806
   287 S      0.573         0.796
   289 A      0.980*        1.145
   290 S      0.943         1.113
   303 I      0.930         1.102
   306 T      0.961*        1.129
   307 A      0.879         1.058
   309 A      0.648         0.860
   312 S      0.888         1.066
   890 S      0.749         0.947

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_CG18304-PC)

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

    78 A      0.650         1.151 +- 0.493
   117 S      0.743         1.261 +- 0.418
   149 I      0.731         1.237 +- 0.447
   214 P      0.586         1.081 +- 0.518
   215 T      0.533         1.023 +- 0.532
   234 L      0.672         1.189 +- 0.459
   274 V      0.555         1.068 +- 0.500
   287 S      0.733         1.251 +- 0.425
   289 A      0.973*        1.479 +- 0.129
   290 S      0.923         1.437 +- 0.223
   301 A      0.507         0.994 +- 0.536
   303 I      0.947         1.456 +- 0.190
   306 T      0.935         1.448 +- 0.203
   307 A      0.874         1.394 +- 0.287
   309 A      0.795         1.311 +- 0.381
   312 S      0.924         1.435 +- 0.231
   591 L      0.560         1.076 +- 0.497
   849 G      0.650         1.157 +- 0.484
   890 S      0.818         1.338 +- 0.351
   908 A      0.522         1.031 +- 0.509
  1020 A      0.553         1.068 +- 0.498