--- 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
