--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun May 27 10:19:27 WEST 2018
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
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/ADOPS1/DNG_A1/NS1_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_A1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_4/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/ADOPS1/DNG_A1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -9005.40         -9052.54
2      -9008.00         -9052.33
--------------------------------------
TOTAL    -9006.02         -9052.44
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_A1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_4/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/ADOPS1/DNG_A1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         7.267033    0.207688    6.316381    8.123070    7.255604    474.90    678.07    1.001
r(A<->C){all}   0.033417    0.000028    0.022876    0.043695    0.033182    745.08    762.79    1.000
r(A<->G){all}   0.243976    0.000309    0.208940    0.276689    0.243568    452.23    539.12    1.001
r(A<->T){all}   0.049546    0.000040    0.037260    0.062083    0.049228    830.91    949.26    1.000
r(C<->G){all}   0.030012    0.000040    0.017701    0.042201    0.029716    884.89    922.87    1.000
r(C<->T){all}   0.619807    0.000426    0.577332    0.657649    0.620377    447.84    515.37    1.001
r(G<->T){all}   0.023242    0.000045    0.011289    0.036639    0.022779    797.58    912.72    1.000
pi(A){all}      0.350688    0.000110    0.330331    0.371544    0.350666    859.01    972.46    1.002
pi(C){all}      0.231045    0.000076    0.213549    0.247780    0.230827    818.35    872.63    1.000
pi(G){all}      0.220174    0.000081    0.202036    0.237744    0.220215    513.91    535.67    1.001
pi(T){all}      0.198093    0.000064    0.182949    0.214077    0.197810    634.96    648.82    1.004
alpha{1,2}      0.212089    0.000187    0.185677    0.239768    0.211622   1320.14   1385.15    1.000
alpha{3}        5.056736    0.873651    3.383337    6.890033    4.948809   1242.73   1335.18    1.000
pinvar{all}     0.136396    0.000505    0.093612    0.180194    0.135518   1385.59   1433.08    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	-8637.396459
Model 2: PositiveSelection	-8637.396459
Model 0: one-ratio	-8760.474374
Model 3: discrete	-8543.545578
Model 7: beta	-8549.940326
Model 8: beta&w>1	-8546.864166


Model 0 vs 1	246.1558299999997

Model 2 vs 1	0.0

Model 8 vs 7	6.152320000001055

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: gb:GQ398258|Organism:Dengue_virus_2|Strain_Name:DENV-2/ID/1016DN/1975|Protein_Name:Nonstructural_protein_NS1|Gene_Symbol:NS1)

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

    94 K      0.670         0.752
    98 Q      0.687         0.764
   128 L      0.978*        0.983
   131 Q      0.899         0.924
   178 F      0.970*        0.978
   224 H      0.579         0.683

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: gb:GQ398258|Organism:Dengue_virus_2|Strain_Name:DENV-2/ID/1016DN/1975|Protein_Name:Nonstructural_protein_NS1|Gene_Symbol:NS1)

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

   128 L      0.717         1.267 +- 0.392
   178 F      0.772         1.316 +- 0.374