--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Nov 08 18:16:35 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/176/CG6420-PB/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/176/CG6420-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/176/CG6420-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/176/CG6420-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -9602.84         -9617.78
2      -9602.60         -9619.30
--------------------------------------
TOTAL    -9602.71         -9618.80
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/176/CG6420-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/176/CG6420-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/176/CG6420-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}         1.085472    0.003190    0.973200    1.191929    1.083646   1367.55   1434.28    1.000
r(A<->C){all}   0.090568    0.000105    0.070759    0.110727    0.090273    990.28   1018.26    1.000
r(A<->G){all}   0.242567    0.000381    0.206252    0.282350    0.242804    915.09    939.02    1.000
r(A<->T){all}   0.135538    0.000402    0.095332    0.174545    0.134991    793.68    858.74    1.001
r(C<->G){all}   0.041925    0.000035    0.030618    0.053773    0.041687   1030.76   1099.01    1.000
r(C<->T){all}   0.417995    0.000596    0.373609    0.468516    0.417065    846.79    868.62    1.000
r(G<->T){all}   0.071407    0.000131    0.049278    0.092391    0.071115    817.37    856.03    1.000
pi(A){all}      0.207832    0.000051    0.193958    0.221732    0.207717   1093.74   1118.15    1.000
pi(C){all}      0.342174    0.000064    0.326603    0.357082    0.342265   1046.57   1081.30    1.000
pi(G){all}      0.304305    0.000064    0.289570    0.320764    0.304254    856.55    960.37    1.001
pi(T){all}      0.145690    0.000036    0.134580    0.157916    0.145492    962.77   1072.25    1.001
alpha{1,2}      0.132146    0.000091    0.115050    0.152598    0.131487   1145.17   1209.76    1.000
alpha{3}        4.857435    1.131455    3.122698    7.127632    4.733235   1499.09   1500.05    1.000
pinvar{all}     0.354794    0.000677    0.303026    0.404190    0.355923   1226.18   1363.59    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	-8474.654177
Model 2: PositiveSelection	-8471.868255
Model 0: one-ratio	-8572.23055
Model 3: discrete	-8461.115123
Model 7: beta	-8475.317347
Model 8: beta&w>1	-8461.387317


Model 0 vs 1	195.15274599999975

Model 2 vs 1	5.5718440000018745

Model 8 vs 7	27.860059999999066

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_CG6420-PB)

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

    66 S      0.740         2.053
    70 T      0.992**       2.658
    72 V      0.632         1.795
    75 T      0.996**       2.668
    76 A      0.602         1.719
   550 T      1.000**       2.675
   565 A      0.742         2.058
   570 G      0.973*        2.611
   764 N      0.622         1.770

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_CG6420-PB)

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

    66 S      0.828         1.473 +- 0.573
    68 V      0.647         1.230 +- 0.577
    70 T      0.963*        1.628 +- 0.478
    71 P      0.505         1.038 +- 0.641
    72 V      0.803         1.431 +- 0.547
    75 T      0.969*        1.635 +- 0.473
    76 A      0.782         1.410 +- 0.603
   550 T      0.989*        1.652 +- 0.454
   565 A      0.835         1.477 +- 0.552
   570 G      0.941         1.605 +- 0.501
   764 N      0.779         1.412 +- 0.592