--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun May 06 06:58:53 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_N1/NS1_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_N1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N1/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_N1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8784.56         -8831.50
2      -8784.84         -8826.24
--------------------------------------
TOTAL    -8784.69         -8830.81
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_N1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N1/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_N1/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}         7.859098    0.246382    6.897267    8.819777    7.851632    788.02    795.78    1.000
r(A<->C){all}   0.035675    0.000035    0.024393    0.047464    0.035513    818.93    837.53    1.000
r(A<->G){all}   0.228579    0.000288    0.196318    0.261402    0.227919    647.19    669.95    1.001
r(A<->T){all}   0.057051    0.000049    0.044579    0.071905    0.057026    650.20    797.06    1.001
r(C<->G){all}   0.026606    0.000041    0.014709    0.039701    0.026102    750.18    817.15    1.000
r(C<->T){all}   0.631294    0.000420    0.591301    0.670418    0.631438    589.73    625.70    1.002
r(G<->T){all}   0.020794    0.000044    0.008355    0.033570    0.020314    587.31    614.47    1.000
pi(A){all}      0.353654    0.000108    0.334738    0.374872    0.353637    859.70    861.66    1.001
pi(C){all}      0.227394    0.000073    0.210091    0.243529    0.227367    799.33    909.86    1.001
pi(G){all}      0.224161    0.000080    0.206173    0.241215    0.224178    733.24    770.07    1.000
pi(T){all}      0.194791    0.000059    0.180878    0.210510    0.194731    841.60    856.84    1.000
alpha{1,2}      0.187140    0.000123    0.164839    0.208179    0.186567   1316.50   1340.33    1.001
alpha{3}        4.385541    0.685596    2.956776    6.167371    4.307881   1338.79   1411.93    1.000
pinvar{all}     0.125640    0.000508    0.082697    0.171496    0.124943   1178.91   1278.24    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	-8246.317649
Model 2: PositiveSelection	-8246.317649
Model 0: one-ratio	-8374.135678
Model 3: discrete	-8140.232408
Model 7: beta	-8145.296777
Model 8: beta&w>1	-8139.917146


Model 0 vs 1	255.63605800000005

Model 2 vs 1	0.0

Model 8 vs 7	10.75926199999958

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:GQ199778|Organism:Dengue_virus_1|Strain_Name:DENV-1/VN/BID-V2754/2007|Protein_Name:nonstructural_protein_1|Gene_Symbol:NS1)

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

   129 T      0.684         1.250 +- 0.439
   176 V      0.864         1.444 +- 0.396