--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri May 25 03:02:23 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_1/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_A1/NS1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8578.98         -8625.61
2      -8576.99         -8635.01
--------------------------------------
TOTAL    -8577.56         -8634.32
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_A1/NS1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         7.061918    0.217229    6.119356    7.933400    7.046622    588.49    600.44    1.000
r(A<->C){all}   0.031058    0.000031    0.020392    0.042085    0.030903    704.83    786.88    1.000
r(A<->G){all}   0.227081    0.000289    0.195949    0.260514    0.227040    606.11    660.73    1.000
r(A<->T){all}   0.056509    0.000052    0.043015    0.070569    0.056291    677.10    769.34    1.000
r(C<->G){all}   0.022135    0.000039    0.011028    0.034886    0.021683    709.93    734.92    1.001
r(C<->T){all}   0.635477    0.000411    0.596931    0.674172    0.635463    434.52    575.90    1.000
r(G<->T){all}   0.027740    0.000051    0.014001    0.041716    0.027284    746.40    746.72    1.000
pi(A){all}      0.347892    0.000109    0.327683    0.368054    0.347799    758.57    970.62    1.000
pi(C){all}      0.228362    0.000079    0.209986    0.244634    0.228234    765.18    794.12    1.000
pi(G){all}      0.226861    0.000088    0.209940    0.245728    0.226704    671.77    721.30    1.001
pi(T){all}      0.196886    0.000060    0.180936    0.211466    0.196766    898.71    957.78    1.000
alpha{1,2}      0.208197    0.000178    0.182822    0.233707    0.207404   1266.30   1279.09    1.000
alpha{3}        5.487497    1.109989    3.615456    7.584599    5.368261   1135.16   1318.08    1.000
pinvar{all}     0.139925    0.000532    0.095227    0.185246    0.139287    915.72   1112.14    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	-8230.639844
Model 2: PositiveSelection	-8230.639844
Model 0: one-ratio	-8359.991238
Model 3: discrete	-8150.736716
Model 7: beta	-8155.178613
Model 8: beta&w>1	-8151.584891


Model 0 vs 1	258.70278800000233

Model 2 vs 1	0.0

Model 8 vs 7	7.187443999999232

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: gb:FJ410223|Organism:Dengue_virus_2|Strain_Name:DENV-2/VN/BID-V1869/2007|Protein_Name:Nonstructural_protein_NS1|Gene_Symbol:NS1)

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

    94 K      0.679         1.227 +- 0.412
   128 S      0.612         1.163 +- 0.438
   131 Q      0.753         1.297 +- 0.369
   178 F      0.561         1.112 +- 0.455