--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Nov 06 13:15:36 WET 2017
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/ZikaADOPSresults/NS4B/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/ZikaADOPSresults/NS4B/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/ZikaADOPSresults/NS4B/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/ZikaADOPSresults/NS4B/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -2939.98 -3000.94
2 -2933.00 -2993.59
--------------------------------------
TOTAL -2933.69 -3000.24
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/ZikaADOPSresults/NS4B/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/ZikaADOPSresults/NS4B/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/ZikaADOPSresults/NS4B/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.416664 0.021894 1.144594 1.704740 1.409123 938.02 1032.41 1.001
r(A<->C){all} 0.029245 0.000074 0.014166 0.047091 0.028204 755.13 838.01 1.000
r(A<->G){all} 0.229793 0.001292 0.161813 0.298938 0.228658 499.34 503.93 1.000
r(A<->T){all} 0.043781 0.000134 0.022925 0.067015 0.042328 711.52 763.36 1.000
r(C<->G){all} 0.009468 0.000025 0.001129 0.019259 0.008778 904.09 947.15 1.001
r(C<->T){all} 0.656395 0.001782 0.576077 0.736875 0.656700 516.25 521.86 1.000
r(G<->T){all} 0.031318 0.000091 0.013531 0.049608 0.030401 803.48 853.26 1.001
pi(A){all} 0.256249 0.000206 0.228777 0.283293 0.256124 1045.58 1093.34 1.000
pi(C){all} 0.263423 0.000210 0.234388 0.291195 0.263694 1110.95 1120.57 1.000
pi(G){all} 0.260052 0.000208 0.232000 0.289091 0.259771 820.09 962.05 1.000
pi(T){all} 0.220276 0.000176 0.197059 0.247857 0.219762 940.37 1020.35 1.001
alpha{1,2} 0.162662 0.000298 0.131484 0.198537 0.160872 819.60 975.68 1.000
alpha{3} 3.022094 0.759642 1.508922 4.766423 2.904284 1096.66 1140.76 1.000
pinvar{all} 0.219410 0.002344 0.125732 0.307428 0.221905 1113.15 1238.73 1.002
------------------------------------------------------------------------------------------------------
* 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 -2745.165193
Model 2: PositiveSelection -2744.894868
Model 0: one-ratio -2795.013585
Model 3: discrete -2744.89476
Model 7: beta -2748.70692
Model 8: beta&w>1 -2744.954962
Model 0 vs 1 99.69678400000066
Model 2 vs 1 0.5406499999999141
Model 8 vs 7 7.503916000000572
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:EU545988|Organism:Zika_virus|Strain_Name:FSM|Protein_Name:nonstructural_protein_NS4B|Gene_Symbol:NS4B)
Pr(w>1) post mean +- SE for w
14 S 0.877 1.036
15 H 0.998** 1.173
19 R 0.815 0.967
23 G 0.840 0.995
24 A 1.000** 1.175
25 T 0.977* 1.149
26 I 1.000** 1.175
87 Y 0.998** 1.173
88 A 1.000** 1.174
91 F 0.934 1.100
98 M 1.000** 1.175
165 R 0.520 0.630
176 I 0.897 1.059
180 V 1.000** 1.174
186 S 0.998** 1.173
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:EU545988|Organism:Zika_virus|Strain_Name:FSM|Protein_Name:nonstructural_protein_NS4B|Gene_Symbol:NS4B)
Pr(w>1) post mean +- SE for w
15 H 0.861 1.429 +- 0.411
24 A 0.955* 1.523 +- 0.294
26 I 0.905 1.475 +- 0.332
87 Y 0.850 1.417 +- 0.421
88 A 0.791 1.358 +- 0.438
91 F 0.501 0.980 +- 0.614
98 M 0.760 1.327 +- 0.419
180 V 0.784 1.349 +- 0.436
186 S 0.855 1.422 +- 0.414
