--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Oct 28 20:59:37 WEST 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/Zika-NS5/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Zika-NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Zika-NS5/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/Zika-NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8973.35 -9074.81
2 -8979.25 -9068.33
--------------------------------------
TOTAL -8974.04 -9074.12
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Zika-NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Zika-NS5/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/Zika-NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.026702 0.003294 0.914876 1.137509 1.025019 343.20 521.19 1.001
r(A<->C){all} 0.022490 0.000020 0.014138 0.031228 0.022217 438.11 509.46 1.001
r(A<->G){all} 0.211279 0.000468 0.168389 0.252545 0.209929 297.53 337.46 1.002
r(A<->T){all} 0.023549 0.000028 0.014567 0.034567 0.023168 355.44 513.58 1.000
r(C<->G){all} 0.008323 0.000007 0.003509 0.013474 0.008105 836.30 839.21 1.000
r(C<->T){all} 0.714792 0.000611 0.668123 0.764104 0.715825 273.63 325.48 1.002
r(G<->T){all} 0.019567 0.000021 0.010758 0.028433 0.019167 695.68 731.57 1.000
pi(A){all} 0.279748 0.000067 0.264054 0.295969 0.279753 687.16 917.67 1.000
pi(C){all} 0.228624 0.000053 0.214348 0.242190 0.228614 563.44 771.09 1.000
pi(G){all} 0.295676 0.000068 0.279984 0.311741 0.295834 803.72 892.44 1.000
pi(T){all} 0.195952 0.000049 0.181940 0.209339 0.195731 826.73 931.07 1.000
alpha{1,2} 0.124542 0.000093 0.103971 0.142356 0.124305 875.89 1018.98 1.000
alpha{3} 4.945301 1.169899 3.073457 7.173909 4.856330 1178.78 1203.72 1.000
pinvar{all} 0.303807 0.000923 0.246006 0.366706 0.305088 982.38 1025.22 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 -8511.629082
Model 2: PositiveSelection -8502.348666
Model 0: one-ratio -8569.193768
Model 3: discrete -8500.575061
Model 7: beta -8516.270802
Model 8: beta&w>1 -8501.796788
Model 0 vs 1 115.12937199999942
Model 2 vs 1 18.56083199999921
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: gb:KX766029|Organism:Zika virus|Strain Name:R116265|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)
Pr(w>1) post mean +- SE for w
516 R 1.000** 13.211
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:KX766029|Organism:Zika virus|Strain Name:R116265|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)
Pr(w>1) post mean +- SE for w
89 A 0.522 1.257 +- 0.314
135 P 0.643 1.336 +- 0.304
197 Y 0.561 1.243 +- 0.407
261 V 0.645 1.339 +- 0.290
281 S 0.596 1.307 +- 0.301
283 H 0.608 1.314 +- 0.305
289 F 0.525 1.202 +- 0.437
316 I 0.608 1.317 +- 0.284
516 R 0.963* 1.511 +- 0.244
707 H 0.513 1.194 +- 0.432
Model 8 vs 7 28.948027999998885
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:KX766029|Organism:Zika virus|Strain Name:R116265|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)
Pr(w>1) post mean +- SE for w
516 R 1.000** 12.993
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:KX766029|Organism:Zika virus|Strain Name:R116265|Protein Name:RNA-dependent RNA polymerase NS5|Gene Symbol:NS5)
Pr(w>1) post mean +- SE for w
89 A 0.686 1.191 +- 0.480
135 P 0.849 1.362 +- 0.352
190 L 0.506 0.947 +- 0.590
197 Y 0.704 1.187 +- 0.510
261 V 0.878 1.395 +- 0.305
274 N 0.503 0.989 +- 0.539
281 S 0.801 1.314 +- 0.397
283 H 0.810 1.322 +- 0.391
289 F 0.648 1.120 +- 0.544
316 I 0.852 1.371 +- 0.332
516 R 0.999** 1.503 +- 0.067
517 T 0.609 1.108 +- 0.512
692 D 0.549 1.041 +- 0.531
707 H 0.634 1.106 +- 0.548
