--- 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
